Synthesis of tetracyclines and intermediates thereto

ABSTRACT

Efficient method for preparing the enone intermediate (VII) used in the synthesis of tetracyclines derivatives. In particular, the invention provides a synthesis which allows for substituents at positions 4 a , 5, 5 a , and 12 a  of the tetracycline ring system.

PRIORITY INFORMATION

The present application claims priority under 35 U.S.C. §119(e) to U.S. provisional patent applications, U.S. Ser. No. 61/174,185, filed Apr. 30, 2009, and U.S. Ser. No. 61/322,613, filed Apr. 9, 2010, each of which is incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with U.S. Government support under grant ROI AI048825 and predoctoral fellowship GM007598-30 awarded by the National Institutes of Health. The U.S. Government has certain rights in the invention.

BACKGROUND OF THE INVENTION

The tetracyclines are broad spectrum antimicrobial agents that are widely used in humand veterinary medicine (Schappinger et al., “Tetracyclines: Antibiotic Action, Uptake, and Resistance Mechanisms” Arch. Microbiol. 165:359-69, 1996; Mitscher, Medicinal Research Series, Vol. 9, The Chemistry of the Tetracycline Antibiotics, Marcel Dekker Inc. New York, 1978). The total production of tetracyclines by fermentation or semi-synthesis is measured in the thousands of metric tons per year. The first tetracycline, chlorotetracycline (1) (Aureomycin™), was isolated from the soil bacterium Streptomyces aureofaciens by Lederle Laboratories (Wyeth-Ayerst Research) in 1945 (Duggar, Ann. N.Y. Acad. Sci. 51:177-181, 1948; Duggar, Aureomycin and Preparation of Some, U.S. Pat. No. 2,482,055, 1949; incorporated herein by reference). Oxytetracycline (2) was isolated soon after from S. rimosus by scientists at Pfizer Laboratories (Finlay et al., Science 111:85, 1950). The structures of chlorotetracycline and oxytetracycline were elucidated by scientists at Pfizer in collaboration with R. B. Woodward and co-workers at Harvard University (Hochstein et al., J. Am. Chem. Soc. 74:3708-3709, 1952; Hochstein et al., J. Am. Chem. Soc. 75:5455-75, 1953; Stephens et al, J. Am. Chem. Soc. 74:4976-77, 1952; Stephens et al., J. Am. Chem. Soc. 76:3568-75, 1954). Tetracycline (3) was later prepared by the hydrogenolysis of chlorotetracycline and was found to retain the antimicrobial activity of chlorotetracycline and oxytetracycline and had increased stability (Boothe et al. J. Am. Chem. Soc. 75:4621, 1953; Conover et al., J. Am. Chem. Soc. 75:4622-23, 1953). Tetracycline was later found to be a natural product of S. aureofaciens, S. viridofaciens, and S. rimosus.

The primary tetracyclines of clinical importance today include tetracycline (3) (Boothe et al., J. Am. Chem. Soc. 75:4621, 1953), oxytetracycline (2, Terramycin™) (Finlay et al., Science 111:85, 1950), (−)-doxycycline (Stephens et al., J. Am. Chem. Soc. 85:2643, 1963), (−)-minocycline (Martell et al., J. Med. Chem. 10:44, 1967; Martell et al., J. Med. Chem. 10:359, 1967), and tigecycline. The tetracyclines exert their antimicrobial activity by inhibition of bacterial protein synthesis (Bentley and O'Hanlon, Eds., Anti-Infectives: Recent Advances in Chemistry and Structure-Activity Relationships The Royal Society of Chemistry: Cambridge, UK, 1997). Most tetracyclines are bacteriostatic rather than bactericidal (Rasmussen et al., Antimicrob. Agents Chemother. 35:2306-11, 1991; Primrose and Wardlaw, Ed. “The Bacteriostatic and Bacteriocidal Action of Antibiotics” Sourcebook of Experiments for the Teaching of Microbiology Society for General Microbiology, Academic Press Ltd., London, 1982). It has been proposed that after tetracycline passes through the cytoplasmic membrane of a bacterium it chelates Mg⁺², and this tetracycline-Mg⁺² complex binds the 30S subunit of the bacterial ribosome (Goldman et al., Biochemistry 22:359-368, 1983). Binding of the complex to the ribosome inhibits the binding of aminoacyl-tRNAs, resulting in inhibition of protein synthesis (Wissmann et al., Forum Mikrobiol. 292-99, 1998; Epe et al., EMBO J. 3:121-26, 1984). Tetracyclines have also been found to bind to the 40S subunit of eukaryotic ribosome; however, they do not achieve sufficient concentrations in eukaryotic cells to affect protein synthesis because they are not actively transported in eukaryotic cells (Epe et al., FEBS Lett. 213:443-47, 1987).

Structure-activity relationships for the tetracycline antibiotics have been determined empirically from 50 years of semi-synthetic modification of the parent structure (Sum et al., Curr. Pharm. Design 4:119-32, 1998). Permutations of the upper left-hand portion of the natural product, also known as the hydrophobic domain, have provided new therapeutically active agents, while modifications of the polar hydrophobic domain result in a loss of activity. However, semi-synthesis by its very nature has limited the number of tetracycline analogs that can be prepared and studied.

The tetracyclines are composed of four linearly fused six-membered rings with a high density of polar functionality and stereochemical complexity. Previous approaches to the synthesis of tetracyclines typically proceeded via a stepwise assembly of the tetracyclic ring system. In 1962, Woodward and co-workers reported the first total synthesis of racemic 6-desmethyl-6-deoxytetracycline (sancycline, 4), the simplest biologically active tetracycline (Conover et al., J. Am. Chem. Soc. 84:3222-24, 1962). The synthetic route was a remarkable achievement for the time and proceeded by the stepwise construction of the rings in a linear sequence of 22 steps (overall yield ˜0.003%). The first enantioselective synthesis of (−)-tetracycline (3) from the A-ring precursor D-glucosamine (34 steps, 0.002% overall yield) was reported by Tatsuda and co-workers in 2000 (Tatsuta et al., Chem. Lett. 646-47, 2000). Other approaches to the synthesis of tetracycline antibiotics, which have also proceeded by the stepwise assembly of the ABCD ring system beginning with D or CD precursors, include the Shemyakin synthesis of (±)-12a-deoxy-5a,6-anhydrotetracycline (Gurevich et al., Tetrahedron Lett. 8:131, 1967; incorporated herein by reference) and the Muxfeldt synthesis of (±)-5-oxytetracycline (terramycin, 22 steps, 0.06% yield) (Muxfeldt et al., J. Am. Chem. Soc. 101:689, 1979; incorporated herein by reference). Due to the length and poor efficiency of the few existing routes to tetracyclines, which were never designed for synthetic variability, synthesis of tetracycline analogs is still limited.

More recently, a novel convergent synthetic route to tetracyclines and various analogs, including pentacycline and heterocycle-containing tetracyclines, has been developed by Myers and co-workers. See US 2005/0282787, published Dec. 22, 2005; incorporated herein by reference; and Charest et al., Science, 308:395-398, 15 Apr. 2005; Charest et al., J. Am. Chem. Soc. 127:8292-93, 2005. This route proceeds through the highly functionalized chiral enone intermediate (5) which is prepared starting from benzoic acid in ten steps (11% yield, >95% ee) (Charest et al., Science 308:395-398, Apr. 15, 2005; Charest et al., J. Am. Chem. Soc. 127:8292-8293, 2005; Myers et al., Org. Lett. 3(18):2923-26, 2001). A second generation route to the enone intermediate (5) was later developed starting from an isoxazole aldehyde. The second generation route yields the enone in eight steps in an improved yield. See US 2009/0093640, published Apr. 9, 2009; U.S. 60/850,859, filed Oct. 11, 2006; and WO2008/127361, published Oct. 23, 2008; each of which is incorporated herein by reference.

Several approaches were developed to react the enone 5 with a toluate (6), benzylic halide, or benzocyclobutenol (8) to form the tetracycline core ring system. The first approach involves the reaction of the enone with anion formed by the deprotonation of a toluate (6) or metallation of a benzylic halide as shown below.

A second approach involves reacting the enone in a Diels-Alder-type reaction with a diene (7) or a benzocyclobutenol (8).

In these approaches, the chiral enone provides the functionalized A and B rings of the tetracycline core, and the D-ring is derived from the toluate (6), benzylic halide, or benzocyclobutenol (8). In bringing the two portions of the tetracycline core together the C-ring is formed, preferably in a stereoselective manner. These new synthetic approaches to tetracycline analogs not only allow for the stereoselective and efficient synthesis of a wide variety of tetracycline analogs never before prepared, but they also allow for preparation of tetracycline analogs in which the D-ring is replaced with a heterocycle, 5-membered ring, or other ring systems. The new methodologies also allow for the prepartion of various pentacyclines or higher cyclines containing aromatic and non-aromatic carbocycles and heterocycles. See U.S. patent application, US2005/0282782, published Dec. 1, 2005; PCT Application WO 05/112985, published Dec. 1, 2005; and U.S. Provisional Patent Application, U.S. Ser. No. 60/790,413, filed Apr. 7, 2006; each of which is incorporated herein by reference.

A second generation route to the functionalized chiral enone intermediate (9) useful in synthesizing tetracyclines was also recently described by Myers and coworkers (US 2009/0093640, published Apr. 9, 2009; U.S. 60/850,859, filed Oct. 11, 2006; and WO2008/127361, published Oct. 23, 2008; each of which is incorporated herein by reference).

The route yields the highly functionalized chiral enone intermediate (9) in eight steps from an isoxazole aldehyde and allows for the preparation of tetracycline analogs in higher yields that previously attainable.

Although the above approaches to tetracycline analogs are much more efficient than earlier approaches and allow for synthetic variability, there remains a need for improving the efficiency and versatility of these routes to new tetracycline analogs.

SUMMARY OF THE INVENTION

The present invention provides a novel synthetic approach to the functionalized chiral enone of formula (VII) useful in the synthesis of tetracycline analogs. As described herein and in published patent applications (US patent application publication 2005/0282782, published Dec. 1, 2005; international PCT Application WO 2005/112985, published Dec. 1, 2005; international PCT application WO 2007/117639, published Oct. 18, 2007; US patent application publication 2009/0093640, published Apr. 9, 2009; and WO 2008/127361, published Oct. 23, 2008; each of which is incorporated herein by reference), the enone of formula (VII) can be used in various approaches to prepare tetracyclines and analogs thereof. The new synthesis of the enone intermediate, in particular, allows for derivatives with different substituents at positions 4a, 5, 5a, and/or 12a of the tetracycline core to be prepared.

An exemplary synthesis of an enone of formula VII is shown below. The synthesis begins with an isoxazole of formula I and a compound of formula II and in four steps yields enone VII. Isoxazole I is deprotonated and allowed to react with a compound of formula II to give an adduct of formula III, where R_(Q) is, for example, hydrogen, an alkyl moiety, or a silyl moiety. Without work-up or purification, the compound of formula III is treated with a suitable base to induce ring closure and yield a compound of formula IV. A retro Diels-Alder reaction gives a compound of formula V, which is deprotonated and reacted with an electrophile to yield an enone of formula VI. Epimerization at C4 leads to a compound of formula VII. Advantageously, in some embodiments, the use of compounds of formulae II, III, and IV which include at least one silyl moiety at R_(Q) may reduce the temperature at which the retro Diels-Alder reaction is performed compared to when R_(Q) is hydrogen. Additionally or alternatively, such compounds including at least one silyl moiety at R_(Q) may allow synthesis of compounds of formula V in higher yields and/or at reduced reaction times compared to when R_(Q) is hydrogen, as described in more detail below.

Another exemplary synthesis of an enone of formula VII is shown below, where both R_(Q) are hydrogen. The synthesis begins with an isoxazole of formula I and a compound of formula IIA and in four steps yields enone VII. Isoxazole I is deprotonated and allowed to react with a compound of formula IIA to give an adduct of formula IIIA. Without work-up or purification, the compound of formula IIIA is treated with a suitable base to induce ring closure and yield a compound of formula IVA. A retro Diels-Alder reaction gives a compound of formula V, which is deprotonated and reacted with an electrophile to give an enone of formula VI. Epimerization leads to a compound of formula VII.

As would be appreciated by one of skill in the art, various substitutions, derivatives, and modifications of the starting materials, intermediates, reagents, and synthetic methodology may be used to prepare enone VI or VII, or derivatives thereof, without departing from the present invention.

In one aspect, the present invention provides for the synthesis of tetracycline analogs and intermediates thereto wherein either or both of R₁₀ (at position 5a of the tetracycline core) and R₁₁ (at position 4a) are not hydrogen, and also allows for analogs wherein R₉ (at position 12a) is not hydroxyl or a protected or modified hydroxyl. In some embodiments, when R₉ is not hydroxyl or a protected or modified hydroxyl, R₁₀ and R₁₁ are both simultaneously hydrogen. Substituents at positions 4a and 5a include, for example, methyl, trifluoromethyl, methoxymethyl, hydroxyl, methoxy, trifluoromethoxy, amino, alkylamino, azido, methylene, fluorine, and other substituents described herein. Substituents at position 12a include, for example, alkyl, alkoxy, methyl, methoxy, alkylamino, dialkylamino, fluoroalkyl, trifluoromethyl, difluoromethyl, fluoromethyl, and other substituents described herein. Substituents such as methyl or other alkyl groups at position C12a would eliminate the teeth- and bone-staining property of many tetracyclines, which many times prevents the use of these antibiotics in the pediatric population.

In another aspect, the invention provides various useful intermediates in the synthetic scheme leading to enones of the formula VII. Particularly useful intermediates include compounds of the formulae:

The various intermediates with chiral centers are provided in enantiomeric or diasteroemeric pure form or are provided as a mixture of stereoisomers.

The present invention also provides the synthesis of tetracycline analogs using the synthetic methodology for preparing the enone VII, described herein. In certain embodiments, a chiral enone VII prepared by the methodology described herein is used in combination with the methodologies described in US 2005/0292787, which is incorporated herein by reference, to prepare a tetracycline analog. In certain embodiments, the inventive methods of synthesis of the enone intermediate is used to synthesize any compound described in U.S. patent application, US 2005/0282787, published Dec. 22, 2005; international PCT application, WO 05/112945, published Dec. 1, 2005; U.S. provisional patent application, U.S. Ser. No. 60/790,413, filed Apr. 7, 2006; international PCT application, WO 07/117,639, published Oct. 18, 2007; or international PCT application, WO 08/127,361, published Oct. 23, 2008; each of which is incorporated herein by reference. The inventive methods and intermediates may also be used to prepare tetracyclines or tetracycline analogs known in the art (e.g., doxycycline, sancycline, minocycline, tigecycline, tetracycline, etc.). The new synthetic approach to the enone intermediate is particularly useful in preparing 6-deoxytetracyclines. The new synthetic methodology and intermediates are also useful in preparing 6-hydroxytetracyclines, pentacyclines, hexacyclines, C5-substituted tetracyclines, C5-unsubstituted tetracyclines, C5a-substituted tetracyclines, C4a-substituted tetracyclines, C12a-substituted tetracyclines, tetracyclines with heterocyclic b-rings, and other tetracycline analogs. Such structures may include R₉, R₁₀, and substituents, wherein one or more of the following conditions are met: i) R₉ is not hydroxyl or a protected hydroxyl; ii) R₁₀ is not hydrogen; and iii) R₁₁ is not hydrogen. As would be appreciated by one of skill in this art, the new synthesis of enone VII is also useful in preparing other organic compounds which may or may not be related to tetracyclines.

Some of the broad classes of compounds available through these new approaches and considered to be a part of the present invention include tetracyclines and various analogs with substituents at positions 4a, 5, 5a, and/or 12a of the tetracycline ring system, wherein substituents at the 12a (R₉) position is not —OR_(C), or substituents at the 5a (R₁₀) and 4a (R₁₁) positions are not simultaneously hydrogen. Important subclasses of tetracyclines include 6-deoxytetracyclines with or without a C5-hydroxyl group, and 6-hydroxytetracyclines with or without a C5-hydroxyl group. Many of the analogs available through these new approaches have never been synthesized before given the limitations of semi-synthetic approaches and earlier total syntheses. For example, certain substitutions about the D-ring become accessible using the present invention's novel methodologies. In certain classes of compounds of the invention, the D-ring of the tetracyclines analog, which is usually a phenyl ring, is replaced with a heterocyclic moiety, which may be bicyclic or tricyclic. In other classes, the D-ring is replaced with a non-aromatic ring. The size of the D-ring is also not limited to six-membered rings, but instead it may be three-membered, four-membered, five-membered, seven-membered, or larger. In the case of pentacyclines, the five rings may or may not be linear in arrangement. Each of the D- and E-rings may be heterocyclic or carbocyclic, may be aromatic or non-aromatic, and may contain any number of atoms ranging from three to ten atoms. In addition, higher cyclines such as hexacyclines may be prepared. In certain classes, the C-ring may not be fully formed, leading to dicyclines with the A-B fused ring system intact. The compounds of the invention include isomers, stereoisomers, enantiomers, diastereomers, tautomers, protected forms, pro-drugs, salts, and derivatives of any particular compound.

In certain embodiments, the invention provides several basic approaches to the synthesis of tetracycline analogs using the synthesis described herein for preparing the enone intermediate. The first approach to preparing tetracycline analogs involves reaction of the enone with anion formed by the deprotonation of a toluate or metalation of a benzylic halide. The deprotonation of a toluate is particularly useful in preparing 6-deoxytetracyclines with or without a C5-substituent. The metalation (e.g., metal-halogen exchange (e.g., lithium-halogen exchange), metal-metalloid exchange (e.g., lithium-metalloid exchange) is particularly useful in preparing 6-deoxytetracyclines with or without a C5-substituent as well as pentacyclines. The second approach to preparing tetracycline analogs involves reacting the enone intermediate, as prepared by the inventive methodology, in a Diels-Alder-type reaction with a diene or a benzocyclobutenol. In both of these approaches, the chiral enone provides the functionalized A and B rings of the tetracycline core, and the D-ring is derived from the toluate, benzylic halide, or benzocyclobutenol. In bringing these two portions of the molecule together the C-ring is formed. In certain embodiments, the C-ring is formed in a stereoselective manner. These approaches not only allow for the stereoselective and efficient synthesis of a wide variety of tetracycline analogs, but they also allow for the efficient preparation of tetracycline analogs in which the D-ring is replaced with a heterocycle, 5-membered ring, or other ring system. They also allow the preparation of various pentacyclines or higher cyclines containing aromatic and non-aromatic carbocycles and heterocycles. These approaches also allow for the preparation of various tricyclines.

In certain embodiments, the inventive intermediates (e.g., enone, derivatives of enone, dicyclines) have biological activity. For example, an intermediate may possess anti-microbial or anti-proliferative activity. In another aspect, the present invention provides methods of treatment and pharmaceutical compositions including the novel compounds of the present invention. The pharmaceutical compositions may optionally include a pharmaceutically acceptable excipient. The methods and pharmaceutical compositions may be used to treat any infection including cholera, influenza, bronchitis, acne, malaria, urinary tract infections, sexually transmitted diseases including syphilis and gonorrhea, Legionnaires' disease, Lyme disease, Rocky Mountain spotted fever, Q fever, typhus, bubonic plague, gas gangrene, hospital acquired infections, leptospirosis, whooping cough, and anthrax. In certain embodiments, the infections are caused by tetracycline-resistant organisms. In certain instances, the compounds of the invention exhibit anti-neoplastic or anti-proliferative activity, in which case the compounds may be useful in the treatment of diseases such as cancer, autoimmune diseases, inflammatory diseases, and diabetic retinopathy. The methods and compositions may be used to treat disease in humans and other animals including domesticated animals. Any mode of administration including oral and parenteral administration of a pharmaceutical composition comprising an inventive compound may be used.

In some embodiments, tetracycline analogs having non-hydrogen substituents at position C4a and/or C12a have reduced metabolism or phototransformation to B-ring quinone derivatives as compared to known tetracyclines. A reduction in this undesired chemistry may reduce photosensitivity and teeth-staining properties of tetracycline analogs.

Given the versatility and efficiency of the synthesis of tetracycline analogs using enone VII as an intermediate, the present invention represents an improvement in the overall synthetic approach to tetracycline analogs. The present invention allows for the preparation of tetracycline analogs in higher yields than previously attainable and allows for the synthesis of novel tetracycline analogs that were previously inaccessible. The new synthetic approach to the enone intermediate also makes the synthesis of tetracycline analogs more amenable to large-scale production given its improved overall yield. In some embodiments, the present invention provides new synthetic methods to enones of formula VII, new intermediates to enones of formula VII, and/or new tetracycline analogs and the synthesis of the same from enones of formula VII.

DEFINITIONS

Definitions of specific functional groups and chemical terms are described in more detail below. For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^(th) Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito: 1999; Strategic Applications of Named Reactions in Organic Synthesis, Laszlo Kurti and Barbara Czako, Academic Press, 1^(st) edition: Mar. 18, 2005; Comprehensive Organic Transformations: A Guide to Functional Group Preparations, Richard C. Larock, Wiley-VCH, 2^(nd) edition: Nov. 3, 1999; Name Reactions of Functional Group Transformations, Comprehensive Name Reactions, Jie Jack Li and E. J. Corey, Wiley: Jul. 16, 2007; Greene's Protective Groups in Organic Synthesis, Peter G. M. Wuts and Theodora W. Greene, Wiley-Interscience, 4^(th) edition: Oct. 30, 2006; and March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Michael B. Smith and Jerry March, Wiley-Interscience, 6^(th) edition: Jan. 16, 2007, the entire contents of which are incorporated herein by reference.

It should be understood that any atom described herein includes all isotope forms of that atom. For example, —H may be —¹H, —²H (-D), —³H, etc. Accordingly, the structures described herein include all isotopologues thereof.

Certain compounds of the present invention may exist in particular geometric or stereoisomeric forms. The present invention contemplates all such compounds, including cis- and trans-isomers, R- and S-enantiomers, diastereomers, (D)-isomers, (L)-isomers, the racemic mixtures thereof, and other mixtures thereof, as falling within the scope of the invention. Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in this invention.

Isomeric mixtures containing any of a variety of isomer ratios may be utilized in accordance with the present invention. For example, where only two isomers are combined, mixtures containing 50:50, 60:40, 70:30, 80:20, 90:10, 95:5, 96:4, 97:3, 98:2, 99:1, or 100:0 isomer ratios are all contemplated by the present invention. Those of ordinary skill in the art will readily appreciate that analogous ratios are contemplated for more complex isomer mixtures.

If, for instance, a particular enantiomer of a compound of the present invention is desired, it may be prepared by asymmetric synthesis, or by derivation with a chiral auxiliary, where the resulting diastereomeric mixture is separated and the auxiliary group cleaved to provide the pure desired enantiomers. Alternatively, where the molecule contains a basic functional group, such as amino, or an acidic functional group, such as carboxyl, diastereomeric salts are formed with an appropriate optically-active acid or base, followed by resolution of the diastereomers thus formed by fractional crystallization or chromatographic means well known in the art, and subsequent recovery of the pure enantiomers.

One of ordinary skill in the art will appreciate that the synthetic methods, as described herein, utilize a variety of protecting groups. By the term “protecting group”, as used herein, it is meant that a particular functional moiety, e.g., O, S, or N, is temporarily blocked so that a reaction can be carried out selectively at another reactive site in a multifunctional compound. In preferred embodiments, a protecting group reacts selectively in good yield to give a protected substrate that is stable to the projected reactions; the protecting group should be selectively removable in good yield by readily available, preferably non-toxic reagents that do not attack the other functional groups; the protecting group forms an easily separable derivative (more preferably without the generation of new stereogenic centers); and the protecting group has a minimum of additional functionality to avoid further sites of reaction. As detailed herein, oxygen, sulfur, nitrogen, and carbon protecting groups may be utilized. Hydroxyl protecting groups include methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3-bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4-methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl, 4-methoxytetrahydrothiopyranyl S,S-dioxide, 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP), 1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiopyranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl, 1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl, t-butyl, allyl, p-chlorophenyl, p-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), p-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N-oxido, diphenylmethyl, p,p′-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, α-naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl, di(p-methoxyphenyl)phenylmethyl, tri(p-methoxyphenyl)methyl, 4-(4′-bromophenacyloxyphenyl)diphenylmethyl, 4,4′,4″-tris(4,5-dichlorophthalimidophenyl)methyl, 4,4′,4″-tris(levulinoyloxyphenyl)methyl, 4,4′,4″-tris(benzoyloxyphenyl)methyl, 3-(imidazol-1-yl)bis(4′,4″-dimethoxyphenyl)methyl, 1,1-bis(4-methoxyphenyl)-1′-pyrenylmethyl, 9-anthryl, 9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl, 1,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, t-butyldimethylsilyl (TBDMS), t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl, diphenylmethylsilyl (DPMS), t-butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p-phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl)ethyl carbonate (Psec), 2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate, 4-ethoxy-1-naphthyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate, 4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl, 4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate, o-(methoxycarbonyl)benzoate, α-naphthoate, nitrate, alkyl N,N,N′,N′-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts). For protecting 1,2- or 1,3-diols, the protecting groups include methylene acetal, ethylidene acetal, 1-t-butylethylidene ketal, 1-phenylethylidene ketal, (4-methoxyphenyl)ethylidene acetal, 2,2,2-trichloroethylidene acetal, acetonide, cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal, benzylidene acetal, p-methoxybenzylidene acetal, 2,4-dimethoxybenzylidene ketal, 3,4-dimethoxybenzylidene acetal, 2-nitrobenzylidene acetal, methoxymethylene acetal, ethoxymethylene acetal, dimethoxymethylene ortho ester, 1-methoxyethylidene ortho ester, 1-ethoxyethylidine ortho ester, 1,2-dimethoxyethylidene ortho ester, α-methoxybenzylidene ortho ester, 1-(N,N-dimethylamino)ethylidene derivative, α-(N,N′-dimethylamino)benzylidene derivative, 2-oxacyclopentylidene ortho ester, di-t-butylsilylene group (DTBS), 1,3-(1,1,3,3-tetraisopropyldisiloxanylidene) derivative (TIPDS), tetra-t-butoxydisiloxane-1,3-diylidene derivative (TBDS), cyclic carbonates, cyclic boronates, ethyl boronate, and phenyl boronate. Amino-protecting groups include methyl carbamate, ethyl carbamate, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1-(1-adamantyl)-1-methylethyl carbamate (Adpoc), 1,1-dimethyl-2-haloethyl carbamate, 1,1-dimethyl-2,2-dibromoethyl carbamate (DB-t-BOC), 1,1-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), 1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc), 1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2′- and 4′-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethyl carbamate, t-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz), p-nitrobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyl carbamate, [2-(1,3-dithianyl)]methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc), 1,1-dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate, p-(dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o-nitrophenyl)methyl carbamate, phenothiazinyl-(10)-carbonyl derivative, N′-p-toluenesulfonylaminocarbonyl derivative, N′-phenylaminothiocarbonyl derivative, t-amyl carbamate, S-benzyl thiocarbamate, p-cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate, 2,2-dimethoxycarbonylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate, 1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate, 1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate, 2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p′-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1-methyl-1-cyclopropylmethyl carbamate, 1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate, 1-methyl-1-(p-phenylazophenyl)ethyl carbamate, 1-methyl-1-phenylethyl carbamate, 1-methyl-1-(4-pyridyl)ethyl carbamate, phenyl carbamate, p-(phenylazo)benzyl carbamate, 2,4,6-tri-t-butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, 2,4,6-trimethylbenzyl carbamate, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitrophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (N′-dithiobenzyloxycarbonylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine derivative, o-nitrobenzamide, o-(benzoyloxymethyl)benzamide, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted 1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine, N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N-benzylamine, N-di(4-methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), N²-picolylamino N′-oxide, N-1,1-dimethylthiomethyleneamine, N-benzylideneamine, N-p-methoxybenzylideneamine, N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine, N—(N′,N′-dimethylaminomethylene)amine, N,N′-isopropylidenediamine, N-p-nitrobenzylideneamine, N-salicylideneamine, N-5-chlorosalicylideneamine, N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine, N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine, N-borane derivative, N-diphenylborinic acid derivative, N-[phenyl(pentacarbonylchromium- or tungsten)carbonyl]amine, N-copper chelate, N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide, 3-nitropyridinesulfenamide (Npys), p-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6-trimethyl-4-methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6-dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6-trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms), β-trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4′,8′-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide, trifluoromethylsulfonamide, and phenacylsulfonamide. Exemplary protecting groups are detailed herein, however, it will be appreciated that the present invention is not intended to be limited to these protecting groups; rather, a variety of additional equivalent protecting groups can be readily identified using the above criteria and utilized in the method of the present invention. Additionally, a variety of protecting groups are described in Protective Groups in Organic Synthesis, Fourth Ed. Greene, T. W. and Wuts, P. G., Eds., John Wiley & Sons, New York: 2007, the entire contents of which are hereby incorporated by reference.

It will be appreciated that the compounds, as described herein, may be substituted with any number of substituents or functional moieties. In general, the term “substituted” whether preceded by the term “optionally” or not, and substituents contained in formulas of this invention, refer to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. When more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. As used herein, the term “substituted” is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valencies of the heteroatoms. Furthermore, this invention is not intended to be limited in any manner by the permissible substituents of organic compounds. Combinations of substituents and variables envisioned by this invention are preferably those that result in the formation of stable compounds useful in the treatment, for example, of infectious diseases or proliferative disorders. The term “stable”, as used herein, preferably refers to compounds which possess stability sufficient to allow manufacture and which maintain the integrity of the compound for a sufficient period of time to be detected and preferably for a sufficient period of time to be useful for the purposes detailed herein.

The term “aliphatic”, as used herein, includes both saturated and unsaturated, straight chain (i.e., unbranched), branched, acyclic, cyclic, or polycyclic aliphatic hydrocarbons, which are optionally substituted with one or more functional groups. As will be appreciated by one of ordinary skill in the art, “aliphatic” is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. Thus, as used herein, the term “alkyl” includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as “alkenyl”, “alkynyl”, and the like. Furthermore, as used herein, the terms “alkyl”, “alkenyl”, “alkynyl”, and the like encompass both substituted and unsubstituted groups. In certain embodiments, as used herein, “lower alkyl” is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.

In certain embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-4 carbon atoms. Illustrative aliphatic groups thus include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, —CH₂-cyclopropyl, vinyl, allyl, n-butyl, sec-butyl, isobutyl, tert-butyl, cyclobutyl, —CH₂-cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert-pentyl, cyclopentyl, —CH₂-cyclopentyl, n-hexyl, sec-hexyl, cyclohexyl, —CH₂-cyclohexyl moieties and the like, which again, may bear one or more substituents. Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, and the like. Representative alkynyl groups include, but are not limited to, ethynyl, 2-propynyl (propargyl), 1-propynyl, and the like.

The term “alkoxy,” or “thioalkyl” as used herein refers to an alkyl group, as previously defined, attached to the parent molecule through an oxygen atom or through a sulfur atom. In certain embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-4 aliphatic carbon atoms. Examples of alkoxy, include but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, tert-butoxy, neopentoxy, and n-hexoxy. Examples of thioalkyl include, but are not limited to, methylthio, ethylthio, propylthio, isopropylthio, n-butylthio, and the like.

The term “alkylamino” refers to a group having the structure —NHR', wherein R′ is aliphatic, as defined herein. In certain embodiments, the aliphatic group contains 1-20 aliphatic carbon atoms. In certain other embodiments, the aliphatic group contains 1-10 aliphatic carbon atoms. In yet other embodiments, the aliphatic group employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the aliphatic group contains 1-6 aliphatic carbon atoms. In yet other embodiments, the aliphatic group contains 1-4 aliphatic carbon atoms. Examples of alkylamino groups include, but are not limited to, methylamino, ethylamino, n-propylamino, iso-propylamino, cyclopropylamino, n-butylamino, tert-butylamino, neopentylamino, n-pentylamino, hexylamino, cyclohexylamino, and the like.

The term “dialkylamino” refers to a group having the structure —NRR′, wherein R and R′ are each an aliphatic group, as defined herein. R and R′ may be the same or different in an dialkylamino moiety. In certain embodiments, the aliphatic groups contains 1-20 aliphatic carbon atoms. In certain other embodiments, the aliphatic groups contains 1-10 aliphatic carbon atoms. In yet other embodiments, the aliphatic groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the aliphatic groups contains 1-6 aliphatic carbon atoms. In yet other embodiments, the aliphatic groups contains 1-4 aliphatic carbon atoms. Examples of dialkylamino groups include, but are not limited to, dimethylamino, methyl ethylamino, diethylamino, methylpropylamino, di(n-propyl)amino, di(iso-propyl)amino, di(cyclopropyl)amino, di(n-butyl)amino, di(tert-butyl)amino, di(neopentyl)amino, di(n-pentyl)amino, di(hexyl)amino, di(cyclohexyl)amino, and the like. In certain embodiments, R and R′ are linked to form a cyclic structure. The resulting cyclic structure may be aromatic or non-aromatic. Examples of cyclic diaminoalkyl groups include, but are not limited to, aziridinyl, pyrrolidinyl, piperidinyl, morpholinyl, pyrrolyl, imidazolyl, 1,3,4-trianolyl, and tetrazolyl.

Some examples of substituents of the above-described aliphatic (and other) moieties of compounds of the invention include, but are not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; F; Cl; Br; I; —OH; —N₃; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂OR_(x); —CH₂N(R_(x))₂; ═C(R_(x))₂; —CH₂R_(x); —CH₂CH₂OH; —CH₂NH₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OC(R_(x))₃; —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x) wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, haloaliphatic, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, haloaliphatic, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substituents are illustrated by the specific embodiments shown in the Examples that are described herein.

In general, the terms “aryl” and “heteroaryl,” as used herein, refer to stable mono- or polycyclic, heterocyclic, polycyclic, and polyheterocyclic unsaturated moieties having preferably 3-14 carbon atoms, each of which may be substituted or unsubstituted. Substituents include, but are not limited to, any of the previously mentioned substitutents, i.e., the substituents recited for aliphatic moieties, or for other moieties as disclosed herein, resulting in the formation of a stable compound. In certain embodiments of the present invention, “aryl” refers to a mono- or bicyclic carbocyclic ring system having one or two aromatic rings including, but not limited to, phenyl, naphthyl, tetrahydronaphthyl, indanyl, indenyl, and the like. In certain embodiments of the present invention, the term “heteroaryl”, as used herein, refers to a cyclic aromatic radical having from five to ten ring atoms of which one ring atom is selected from S, O, and N; zero, one, or two ring atoms are additional heteroatoms independently selected from S, O, and N; and the remaining ring atoms are carbon, the radical being joined to the rest of the molecule via any of the ring atoms, such as, for example, pyridyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, and the like.

It will be appreciated that aryl and heteroaryl groups can be unsubstituted or substituted, wherein substitution includes replacement of one, two, three, or more of the hydrogen atoms thereon independently with any one or more of the following moieties including, but not limited to: aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; —F; —Cl; —Br; —I; —OH; —N₃; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂OR_(x); —CH₂R_(x); —CH₂CH₂OH; —CH₂NH₂; —CH₂N(R_(x))₂; ═C(R_(x))₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OC(R_(x))₃; —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x), wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, haloaliphatic, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, haloaliphatic, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples that are described herein.

The term “cycloalkyl,” as used herein, refers specifically to groups having three to seven, preferably three to ten carbon atoms. Suitable cycloalkyls include, but are not limited to cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and the like, which, as in the case of other aliphatic, heteroaliphatic, haloaliphatic, or heterocyclic moieties, may optionally be substituted with substituents including, but not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; —F; —Cl; —Br; —I; —OH; —N₃; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂OR_(x); —CH₂R_(x); —CH₂CH₂OH; —CH₂NH₂; —CH₂N(R_(x))₂; ═C(R_(x))₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OC(R_(x))₃; —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x), wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, haloaliphatic, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, haloaliphatic, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples that are described herein.

The term “heteroaliphatic,” as used herein, refers to aliphatic moieties that contain one or more oxygen, sulfur, nitrogen, phosphorus, or silicon atoms, e.g., in place of carbon atoms. Heteroaliphatic moieties may be branched, unbranched, cyclic or acyclic and include saturated and unsaturated heterocycles such as morpholino, pyrrolidinyl, etc. In certain embodiments, heteroaliphatic moieties are substituted by independent replacement of one or more of the hydrogen atoms thereon with one or more moieties including, but not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; —F; —Cl; —Br; —I; —OH; —N₃; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂OR_(x); —CH₂R_(x); —CH₂CH₂OH; —CH₂NH₂; —CH₂N(R_(x))₂; ═C(R_(x))₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OC(R_(x))₃; —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x), wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, haloaliphatic, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, haloaliphatic, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples that are described herein.

The terms “halo” and “halogen” as used herein refer to an atom selected from fluorine, chlorine, bromine, and iodine.

The term “haloalkyl” denotes an alkyl group, as defined above, having one, two, or three halogen atoms attached thereto and is exemplified by such groups as chloromethyl, bromoethyl, trifluoromethyl, and the like. The term “haloaliphatic” denotes an aliphatic group, as defined above, having one, two, or three halogen atoms attached thereto.

The term “heterocycloalkyl” or “heterocycle,” as used herein, refers to a non-aromatic 5-, 6-, or 7-membered ring or a polycyclic group, including, but not limited to a bi- or tri-cyclic group comprising fused six-membered rings having between one and three heteroatoms independently selected from oxygen, sulfur and nitrogen, wherein (i) each 5-membered ring has 0 to 1 double bonds and each 6-membered ring has 0 to 2 double bonds, (ii) the nitrogen and sulfur heteroatoms may be optionally be oxidized, (iii) the nitrogen heteroatom may optionally be quaternized, and (iv) any of the above heterocyclic rings may be fused to a benzene ring. Representative heterocycles include, but are not limited to, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, and tetrahydrofuryl. In certain embodiments, a “substituted heterocycloalkyl or heterocycle” group is utilized and as used herein, refers to a heterocycloalkyl or heterocycle group, as defined above, substituted by the independent replacement of one, two or three of the hydrogen atoms thereon with but are not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; —F; —Cl; —Br; —I; —OH; —N₃; —NO₂; —CN; —CF₃; —CH₂CF₃; —CHCl₂; —CH₂OH; —CH₂OR_(x); —CH₂R_(x); —CH₂CH₂OH; —CH₂NH₂; —CH₂N(R_(x))₂; ═C(R_(x))₂; —CH₂SO₂CH₃; —C(O)R_(x); —CO₂(R_(x)); —CON(R_(x))₂; —OC(O)R_(x); —OCO₂R_(x); —OC(R_(x))₃; —OCON(R_(x))₂; —N(R_(x))₂; —S(O)₂R_(x); —NR_(x)(CO)R_(x), wherein each occurrence of R_(x) independently includes, but is not limited to, aliphatic, heteroaliphatic, haloaliphatic, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, haloaliphatic, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples which are described herein.

“Carbocycle”: The term “carbocycle,” as used herein, refers to an aromatic or non-aromatic ring in which each atom of the ring is a carbon atom.

“Independently selected”: The term “independently selected” is used herein to indicate that the R groups can be identical or different.

“Labeled”: As used herein, the term “labeled” is intended to mean that a compound has at least one element, isotope, or chemical compound attached to enable the detection of the compound. In general, labels typically fall into three classes: a) isotopic labels, which may be radioactive or heavy isotopes, including, but not limited to, ²H, ³H, ³²P, ³⁵S, ⁶⁷Ga, ^(99m)Tc (tc-99m), ¹¹¹In, ¹²³I, ¹²⁵I, ¹⁶⁹Yb and ¹⁸⁶Re; b) immune labels, which may be antibodies or antigens, which may be bound to enzymes (such as horseradish peroxidase) that produce detectable agents; and c) colored, luminescent, phosphorescent, or fluorescent dyes. It will be appreciated that the labels may be incorporated into the compound at any position that does not interfere with the biological activity or characteristic of the compound that is being detected. In certain embodiments, hydrogen atoms in the compound are replaced with deuterium atoms (²H) to slow the degradation of compound in vivo. Due to isotope effects, enzymatic degradation of the deuterated tetracyclines may be slowed thereby increasing the half-life of the compound in vivo. The term “isotopologue” refers to a species that has the same chemical structure and formula as a specific compound of this invention, with the exception of the isotopic composition at one or more positions, e.g., H vs. D. Thus, an isotopologue differs from a specific compound of this invention in the isotopic composition thereof. In certain embodiments of the invention, photoaffinity labeling is utilized for the direct elucidation of intermolecular interactions in biological systems. A variety of known photophores can be employed, most relying on photoconversion of diazo compounds, azides, or diazirines to nitrenes or carbenes (See, Bayley, H., Photogenerated Reagents in Biochemistry and Molecular Biology (1983), Elsevier, Amsterdam), the entire contents of which are hereby incorporated by reference. In certain embodiments of the invention, the photoaffinity labels employed are o-, m- and p-azidobenzoyls, substituted with one or more halogen moieties, including, but not limited to 4-azido-2,3,5,6-tetrafluorobenzoic acid.

“Tautomers”: As used herein, the term “tautomers” are particular isomers of a compound in which a hydrogen and double bond have changed position with respect to the other atoms of the molecule. For a pair of tautomers to exist there must be a mechanism for interconversion. Examples of tautomers include keto-enol forms, imine-enamine forms, amide-imino alcohol forms, amidine-aminidine forms, nitroso-oxime forms, thio ketone-enethiol forms, N-nitroso-hydroxyazo forms, nitro-aci-nitro forms, and pyridione-hydroxypyridine forms.

Definitions of non-chemical terms used throughout the specification include:

“Animal”: The term animal, as used herein, refers to humans as well as non-human animals, including, for example, mammals, birds, reptiles, amphibians, and fish. Preferably, the non-humanimal is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a primate, or a pig). A non-humanimal may be a transgenic animal.

“Associated with”: When two entities are “associated with” one another as described herein, they are linked by a direct or indirect covalent or non-covalent interaction. Preferably, the association is covalent. Desirable non-covalent interactions include hydrogen bonding, van der Waals interactions, hydrophobic interactions, magnetic interactions, electrostatic interactions, etc.

“Effective amount”: In general, the “effective amount” of an active agent refers to an amount sufficient to elicit the desired biological response. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound of the invention may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the mode of administration, and the patient. For example, the effective amount of a tetracycline analog antibiotic is the amount that results in a sufficient concentration at the site of the infection to kill the microorganism causing the infection (bacteriocidal) or to inhibit the reproduction of such microorganisms (bacteriostatic). In another example, the effective amount of tetracycline analog antibiotic is the amount sufficient to reverse clinicals signs and symptoms of the infection, including fever, redness, warmth, pain, chills, cultures, and pus production.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows a setup for a continuous flow reaction useful in converting a compound of formula IV or IVA into a compound of formula V.

FIGS. 2-7 are tables showing IC₅₀ values for tetracyclines described herein tested with various Gram-positive and Gram-negative bacterial strains.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTION

The present invention provides a strategy for the synthesis of tetracycline analogs (particularly, position 4a, 5, 5a, and 12a analogs) via a convergent synthesis using, as an intermediate, the highly functionalized chiral enone VII as shown below:

wherein

R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); ═O; —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —NO₂; —N₃; —N(R_(B))₂; —NHC(O)R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

R₅, R₉, R₁₀, and R₁₁ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —NO₂; —N₃; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and

R_(P) is hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In embodiments in which R₉ is not —OR_(C), the enone may have the formula:

wherein R₉′ is hydrogen; a halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —NO₂; —N₃; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and

R₃, R₄, R₅, R₁₀, R₁₁, and R_(P) are as defined above and described herein.

In embodiments in which R₁₀ is not hydrogen, the enone may have the formula:

wherein R₁₀′ is a halogen but not hydrogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —NO₂; —N₃; —N(R_(C))₂; —NHC(O)R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and

R₃, R₄, R₅, R₉, R₁₁, and R_(P) are as defined above and described herein.

In embodiments in which R₁₁ is not hydrogen, the enone may have the formula:

wherein R₁₁′ is a halogen but not hydrogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —NO₂; —N₃; —N(R_(C))_(2i)—NHC(O)R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and

R₃, R₄, R₅, R₉, R₁₀, and R_(P) are as defined above and described herein.

The chiral enone of formulas VII, VII′, VII″, and VII′″ can be reacted with anions of phthalides, anions of toluates, benzocyclobutenole, or dienes to yield tetracycline analogs including tetracyclines, heterocyclic tetracyclines, pentacyclines, heterocyclic pentacyclines, tricyclines, polycyclines, and heterocyclic polycyclines. The new compounds are expected to have anti-microbial activity and/or antiproliferative activity, and may be tested for anti-microbial activity against microbes including traditionally tetracycline-sensitive organisms as well as organisms known to be tetracycline-resistant. Compounds found to be bacteriocidal or bacteriostatic may be used in formulating pharmaceutical compositions for the treatment of infections in humand veterinary medicine. The compounds may also be tested for antiproliferative activity. Compounds described herein may be useful in the treatment of proliferative diseases including cancer, anti-inflammatory diseases, autoimmune diseases, benign neoplasms, and diabetic retinopathy, as well as other diseases and conditions. The inventive approach to the synthesis of tetracycline analogs allows for the efficient synthesis of many compounds never before prepared or available using earlier routes and semi-synthetic techniques.

In some embodiments, tetracycline analogs having non-hydrogen substituents at position C4a or C12a are precluded from metabolism or phototransformation to B-ring quinone derivatives, unlike known tetracyclines. This undesired chemistry leads to photosensitivity and teeth-staining properties, preventing the use of tetracyclines in children.

Compounds

Compounds of the present invention include tetracycline analogs, heterocyclic tetracycline analogs, dicyclines, tricyclines, pentacyclines, heterocylic pentacyclines, bridged pentacyclines, heterocyclic polycyclines, bridged polycyclines, and other polycyclines. In certain embodiments, the compounds of the invention exhibit antimicrobial activity. For example, the compound may have a mean inhibitory concentration, with respect to a particular bacteria, of less than 50 μg/mL, preferably less than 25 μg/mL, more preferably less than 5 μg/mL, and most preferably less than 1 μg/mL. For example, infection caused by the following organisms may be treated with antimicrobial compounds of the invention: Gram-positives—Staphylocococcus aureus, Streptococcus Group A, Streptococcus viridans, Streptococcus pneumoniae; Gram-negatives—Neisseria meningitidis, Neisseria gonorrhoeae, Haemophilus influenzae, Escherichia coli, Bacteroides fragilis, other Bacteroides; and Others—Mycoplasma pneumoniae, Treponema pallidum, Rickettsia, and Chlamydia. In other embodiments, the compounds of the invention exhibit antiproliferative activity.

In certain embodiments, the tetracycline analogs of the present invention are represented by the formula:

or a pharmaceutically acceptable salt thereof; wherein

represents a single or double bond;

R₁ and R₂ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(A); —CH₂OR_(A); —CH₂N(R_(A))₂; ═C(R_(A))₂; —CH₂R_(A); —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —N₃; —NO₂; —N(R_(A))₂; —NHC(O)R_(A); —NHSO₂R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₁ and R₂ are taken together to form ═O;

R₃, R₄, R₅, R₉, R₁₀, and R₁₁ are defined herein;

R₇ is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

R₆ and R₈ are absent if the dashed line between the carbon atoms to which R₆ and R₈ are attached represents a bond, or are each independently hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —NO₂, amino, alkylamino, or dialkylamino;

each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and

n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In embodiments in which R₉ is not —OR_(C), the tetracycline analog may have the formula:

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₉′, R₁₀, R₁₁, and R_(P) are as defined above and described herein, and n is an integer in the range of 0 to 8, inclusive.

In embodiments in which R₁₀ is not hydrogen, the enone may have the formula:

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₉, R₁₀′, R₁₁, and R_(P) are as defined above and described herein, and n is an integer in the range of 0 to 8, inclusive.

In embodiments in which R₁₁ is not hydrogen, the enone may have the formula:

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₉, R₁₀, R₁₁′, and R_(P) are as defined above and described herein, and n is an integer in the range of 0 to 8, inclusive.

In some embodiments, the tetracycline analogs of formula XI are of one of the following formulae:

wherein R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₁₀, and R₁₁ are as defined above and described herein; and

n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

The D-ring of the tetracycline analogs may include one, two, or three double bonds. In certain embodiments, the D-ring is aromatic. In other embodiments, the D-ring includes only one double bond, and in yet other embodiments, the D-ring includes two double bonds which may or may not be in conjugation. The D-ring may be substituted with various groups R₇, R₆, and R₈ as defined above and described herein.

In certain embodiments, R₁ is hydrogen. In other embodiments, R₁ is lower alkyl, alkenyl, or alkynyl. In some embodiments, R₁ is C₁₋₆ alkyl. In yet other embodiments, R₁ is methyl, ethyl, n-propyl, cyclopropyl, or isopropyl. In still other embodiments R₁ is methyl.

In certain embodiments, R₂ is hydrogen. In other embodiments, R₂ is hydroxyl or a protected hydroxyl group. In certain embodiments, R₂ is alkoxy. In yet other embodiments, R₂ is a lower alkyl, alkenyl, or alkynyl group. In some embodiments, R₂ is C₁₋₆ alkyl. In certain embodiments, R₁ is methyl, and R₂ is hydroxyl. In other embodiments, R₁ is methyl, and R₂ is hydrogen. In certain embodiments, R₁ and R₂ are both hydrogen. In certain other embodiments, R₁ and R₂ are taken together to form a carbocyclic or heterocyclic ring system spiro-linked to the C ring of the tetracycline analog.

In certain embodiments, R₃ is hydrogen. In some embodiments, R₃ is halogen. In some embodiments, R₃ is aliphatic. In certain embodiments, R₃ is C₁₋₆ alkyl. In certain embodiments, R₃ is fluorine. In some embodiments, R₃ is —OR_(B). In certain embodiments, embodiments, R₃ is a hydroxyl group or a protected hydroxyl group. In other embodiments, R₃ is alkoxy. In still further embodiments, R₃ is lower alkyl, alkenyl, or alkynyl.

In certain embodiments, R₄ is hydrogen. In some embodiments, R₄ is halogen. In some embodiments, R₄ is aliphatic. In certain embodiments, R₄ is C₁₋₆ alkyl. In certain embodiments, R₄ is fluorine. In some embodiments, R₄ is —OR_(B). In certain embodiments, embodiments, R₄ is a hydroxyl group or a protected hydroxyl group. In other embodiments, R₄ is alkoxy. In still further embodiments, R₄ is lower alkyl, alkenyl, or alkynyl. In certain embodiments, both R₃ and R₄ are hydrogen. In certain other embodiments, R₃ and R₄ are both fluorine. In yet other embodiments, R₃ and R₄ are taken together to form a carbocyclic or heterocyclic ring system spiro-linked to the B-ring of the tetracycline analog.

In some embodiments, R₅ is —N(R_(C))₂ or —OR_(C). In some embodiments, R₅ is amino, alkylamino, or dialkylamino. In certain embodiments, R₅ is dimethylamino, diethylamino, methyl(ethyl)amino, dipropylamino, methyl(propyl)amino, or ethyl(propyl)amino. In other embodiments, R₅ is (tert-butyldiphenylsilyl)amino. In some embodiments, R₅ is —C(R_(C))₃, wherein R_(C) is as defined and described herein. In some embodiments, R₅ is methylene. In some embodiments, R₅ is —CH₂N(R_(C))₂, wherein R_(C) is as defined and described herein. In some embodiments, R₅ is —CH₂N(CH₃)₂. In other embodiments, R₅ is hydroxyl, protected hydroxyl, or alkoxy. In yet other embodiments, R₅ is sulfhydryl, protected sulfhydryl, or alkylthioxy.

In certain embodiments, R₇ is hydroxyl, protected hydroxyl, alkoxy, lower alkyl, lower alkenyl, lower alkynyl, or halogen. In certain other embodiments, R₇ is —OR_(C), —SR_(C), —N(R_(C))₂, or —NHC(O)R_(C). In yet other embodiments, R₇ is —C(R_(C))₃ or —CH₂R_(C). In some embodiments, R₇ is not a substituted or unsubstituted phenyl ring.

R₆ and R₈ are absent if the dashed line between the carbon atoms to which R₆ and R₈ are attached represents a bond, or are each selected independently from the group consisting of hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —N₃; —NO₂, amino, alkyl amino, and dialkyl amino groups. In certain embodiments, R₆ and R₈ are absent. In other embodiments, R₆ or R₈ is absent. In some embodiments, R₆ and R₈ are each hydrogen.

The variable n is an integer in the range of 0 to 8, inclusive. As will be appreciated by one of skill in the art, when the D-ring is aromatic n is an integer between 0 and 4. In some embodiments, n is an integer between 1 and 3. In certain embodiments, n is an integer between 1 and 2. In certain embodiments, when n is 2, the substituents R₇ are in the ortho configuration. In other embodiments, when n is 2, the substituents R₇ are in the para configuration. In yet other embodiments, when n is 2, the substituents R₇ are in the meta configuration.

In certain embodiments, R₉ is hydrogen. In certain embodiments, R₉ is halogen. In certain embodiments, R₉ is fluorine. In some embodiments, R₉ is —OR_(C). In some embodiments, R₉ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In some embodiments, R₉ is —OC(R_(C))₃ wherein at least one R_(C) is a halogen. In certain embodiments, R₉ is —OCF₃, —OCHF₂, or —OCH₂F. In certain embodiments, R₉ is alkoxy. In certain embodiments, R₉ is C₁₋₆ alkoxy. In certain embodiments, R₉ is methoxy. In certain embodiments, R₉ is ethoxy. In certain embodiments, R₉ is propoxy. In certain embodiments, R₉ is butoxy. In certain embodiments, R₉ is hydroxyl. In other embodiments, R₉ is a protected hydroxyl group. In some embodiments, R₉ is —SR_(C). In some embodiments, R₉ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₉ is alkylthiol. In certain embodiments, R₉ is C₁₋₆ alkylthiol. In certain embodiments, R₉ is methanethiol. In certain embodiments, R₉ is ethanethiol. In certain embodiments, R₉ is propanethiol. In certain embodiments, R₉ is butanethiol. In certain embodiments, R₉ is thiol. In some embodiments, R₉ is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic. In some embodiments, R₉ is acyclic, substituted or unsubstituted, branched or unbranched aliphatic. In some embodiments, R₉ is alkyl. In some embodiments, R₉ is C₁₋₆ alkyl. In certain embodiments, R₉ is methyl. In certain embodiments, R₉ is ethyl. In certain embodiments, R₉ is propyl. In certain embodiments, R₉ is butyl. In certain other embodiments, R₉ is —CF₃, —CHF₂, or —CH₂F. In other embodiments, R₉ is —NH₂. In other embodiments, R₉ is —N(R_(C))₂ or —NH(R_(C)). In certain embodiments, R₉ is alkylamino or dialkylamino.

In some embodiments, R₁₀ is substituted or unsubstituted alkyl. In other embodiments, R₁₀ is —OR_(C). In some embodiments, R₁₀ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In certain embodiments, R₁₀ is alkoxy. In certain embodiments, R₁₀ is C₁₋₆ alkoxy. In certain embodiments, R₁₀ is —CH₂OH. In some embodiments, R₁₀ is an alkoxyalkyl. In some embodiments, R₁₀ is an alkoxymethyl. In some embodiments, R₁₀ is —CH₂OR_(C), wherein R_(C) is as defined and described herein. For instance R_(C) may be —CH₂CH₃OCH₃ in some instances. In certain embodiments, R₁₀ is —CH₂OCH₃. In some embodiments, R₁₀ is methoxymethyl or butoxymethyl. In some embodiments, R₁₀ is —CH₂N(R_(C))₂, wherein R_(C) is as defined and described herein. In some such embodiments, R_(C) is cyclic or heterocyclic. In certain embodiments, R₁₀ is —CH₂N₃. In some embodiments, R₁₀ is morpholinomethyl. In some embodiments, R₁₀ is piperazinylmethyl. In other embodiments, R₁₀ is pyrrolidinomethyl. In some embodiments, R₁₀ is piperidinylmethyl. In some embodiments, R₁₀ is cyclopropylaminomethyl. In other embodiments, R₁₀ is diethylaminomethyl. In some embodiments, R₁₀ is alkylaminomethyl. In some embodiments, R₁₀ is N,N′-hydroxyethylmethylaminomethyl. In some embodiments, R₁₀ is (3-dimethylaminopropyl)aminomethyl. In other embodiments, R₁₀ is N-imidazolylmethyl. In some embodiments, R₁₀ is pyridin-3-aminomethyl. In some embodiments, R₁₀ is aminomethyl. In some embodiments, R₁₀ is acetylaminomethyl. In some embodiments, R₁₀ is N-trimethylacetylaminomethyl. In other embodiments, R₁₀ is N-benzoylaminomethyl. In some embodiments, R₁₀ is N-methyoxyacetylaminomethyl. In some embodiments, R₁₀ is N-3,5-difluorobenzoylaminomethyl. In some embodiments, R₁₀ is N-methanesulfonylaminomethyl. In some embodiments, R₁₀ is —C(═O)R_(C). In other embodiments, R₁₀ is —COOR_(C). In some embodiments, R₁₀ is —C(═O)NR_(C). In certain embodiments, R₁₀ is —CH₂R_(C), where R_(C) is a halogen. In some embodiments, R₁₀ is —CH₂SH. In other embodiments, R₁₀ is —CH₂SCH₃. In certain embodiments, R₁₀ is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, R₁₀ is —N(R_(C))₂. In some embodiments, R₁₀ is —SR_(C). In some embodiments, R₁₀ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₁₀ is alkylthiol. In certain embodiments, R₁₀ is C₁₋₆ alkylthiol. In certain embodiments, R₁₀ is methanethiol. In certain embodiments, R₁₀ is ethanethiol. In certain embodiments, R₁₀ is propanethiol. In certain embodiments, R₁₀ is butanethiol. In certain embodiments, R₁₀ is thiol. In certain embodiments, R₁₀ is hydroxyl. In certain embodiments, R₁₀ is halogen. In other embodiments, R₁₀ is fluorine. In some embodiments, R₁₀ is C₁₋₆ alkyl. In certain embodiments, R₁₀ is methyl. In certain embodiments, R₁₀ is ethyl In certain embodiments, R₁₀ is propyl. In certain embodiments, R₁₀ is butyl. In certain other embodiments, R₁₀ is —CF₃, —CHF₂, or —CH₂F. In certain embodiments, R₁₀ is hydrogen. In other embodiments, R₁₀ is not hydrogen.

In some embodiments, R₁₁ is substituted or unsubstituted alkyl. In other embodiments, R₁₁ is —OR_(C). In yet other embodiments, R₁₁ is —N(R_(C))₂. In some embodiments, R₁₁ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In certain embodiments, R₁₁ is alkoxy. In certain embodiments, R₁₁ is C₁₋₆ alkoxy. In certain embodiments, R₁₁ is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, R₁₁ is —SR_(C). In some embodiments, R₁₁ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₁₁ is alkylthiol. In certain embodiments, R₁₁ is C₁₋₆ alkylthiol. In certain embodiments, R₁₁ is methanethiol. In certain embodiments, R₁₁ is ethanethiol. In certain embodiments, R₁₁ is propanethiol. In certain embodiments, R₁₁ is butanethiol. In certain embodiments, R₁₁ is thiol. In certain embodiments, R₁₁ is hydroxyl, methoxy, or trifluoromethoxy. In certain embodiments, R₁₁ is hydroxyl. In certain embodiments, R₁₁ is halogen. In other embodiments, R₁₁ is fluorine. In some embodiments, R₁₁ is C₁₋₆ alkyl. In certain embodiments, R₁₁ is methyl. In certain embodiments, R₁₁ is ethyl. In certain embodiments, R₁₁ is propyl. In certain embodiments, R₁₁ is butyl. In certain other embodiments, R₁₁ is —CF₃, —CHF₂, or —CH₂F. In certain embodiments, R₁₁ is hydrogen. In other embodiments, R₁₁ is not hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

As will be appreciated by one of skill in this art, compounds of the invention include derivatives, labeled forms, salts, pro-drugs, isomers, and tautomers of the formulae defined and described herein. Derivatives include protected forms. Salts include any pharmaceutically acceptable salts including HCl, HBr, HI, acetate, and fatty acid (e.g., lactate, citrate, myristoleate, oleate, valerate) salts. In certain embodiments, the inventive compound exists in zwitterionic form at neutral pH with the R₅ being a protonated amino group and the C-3 hydroxyl group deprotonated as shown, for example, in formula XIa:

Isomers include geometric isomers, diastereomers, and enantiomers. Tautomers include both keto and enol forms of carbonyl moieties as well as various tautomeric forms of substituted and unsubstituted heterocycles. For example, the B-ring as shown in formula XI includes an enol moiety as drawn, but the enol may exist as the keto form in certain compounds as shown below in formula XIb and XIc:

Other tautomeric forms will be appreciated by one of skill in the art and will depend on the substitution pattern of the core ring structure. The formulae drawn are only given as examples and do not in any way represent the full range of tautomers that may exist for a particular compound.

In certain embodiments, inventive compounds are of formula XId:

or a pharmaceutically acceptable salt thereof;

wherein

, R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₁₀, R_(P), and R_(C) are as defined above and described herein; and

n is an integer in the range of 0 to 8, inclusive; provided that R₁₀ and R₁₁ are not simultaneously hydrogen.

In certain embodiments, inventive compounds are of formula XIe:

or a pharmaceutically acceptable salt thereof;

wherein

, R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₁₁, n, R_(P), and R_(C) are as defined above and described herein.

In certain embodiments, inventive compounds are of formula XIf:

or a pharmaceutically acceptable salt thereof;

wherein

, R₁, R₂, R₃, R₄, R₅, R₆, R₇, R₈, R₉, and R_(P) are as defined above and described herein; and

n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

Various subclasses of compounds of the formula XI which include a substituted or unsubstituted aromatic D-ring are shown below. These subclasses include unsubstituted, monosubstituted, disubstituted, and trisubstituted D-rings.

wherein the definitions of R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀, and R₁₁ are as described above. In certain embodiments, R₇ is hydroxyl, protected hydroxyl, alkoxy, lower alkyl, lower alkenyl, lower alkynyl, or halogen. In other embodiments, R₇ is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; or cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic. In yet other embodiments, R₇ is amino, alkylamino, or dialkylamino. In other embodiments, R₇ is substituted or unsubstituted cyclic, heterocyclic, aryl, or heteroaryl. In certain embodiments, R₇ is branched or unbranched acyl.

Various subclasses of compounds of the formula XI which include a hydroxyl group at C10 are shown:

wherein the definitions of R₁, R₂, R₃, R₄, R₇, R₉, R₁₀, R₁₁, and R_(C) are as defined above and described herein; and

n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In certain embodiments, the compounds are 6-deoxytetracyclines as shown in the formulae below:

wherein the definitions of R₁, R₂, R₃, R₄, R₇, R₉, R₁₀, R₁₁, and R_(C) are as defined above and described herein, and n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Various subclasses of compounds of the formula XI which include a substituted C-ring are shown below:

wherein R₃, R₄, R₉, R₁₀, and R₁₁ are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Various subclasses of compounds of the formula XI that include a substituent at position 5 of the tetracycline core are shown below:

Various subclasses of compounds of the formula XI″ that include a substituent at position 5a of the tetracycline core (wherein R₁₀ is not hydrogen) are shown below:

wherein R₁, R₂, R₃, R₄, R₉, and R₁₁ are as defined above and described herein.

Exemplary compounds of the formula XI that include a substituent at position 5a of the tetracycline core are shown below:

Various subclasses of compounds of the formula XI′″ that include a substituent at position 4a of the tetracycline core (wherein R₁₁ is not hydrogen) are shown below:

wherein R₁, R₂, R₃, R₄, R₉, and R₁₀ are as defined above and described herein.

Various subclasses of compounds of the formula XI that include a substituent at position 12a of the tetracycline core (wherein R₉ is not hydrogen) are shown below:

wherein R₁, R₂, R₃, R₄, R₁₀, and R₁₁ are as defined above and described herein; provided that when the substituent at R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In another aspect of the invention, the carbocyclic D-ring of tetracycline is replaced with a heterocyclic or carbocyclic moiety other than phenyl as shown in formula (XII):

or a pharmaceutically acceptable salt thereof; wherein R₁, R₂, R₃, R₄, R₅, R₉, R₁₀, R₁₁, and R_(P) are defined and described herein;

represents a substituted or unsubstituted aryl, heteroaryl, carbocyclic, or heterocyclic moiety that is not phenyl, in which each occurrence of X is independently —O—, —S—, —NR₇—, or —C(R₇)₂—; n is an integer in the range of 1 to 5, inclusive; and the bonds between adjacent X moieties are either single or double bonds; and

R₇ is absent as valency permits; hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently a hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In embodiments in which R₉ is not —OR_(C), the compound of formula (XII) may have the following structure:

wherein R₁, R₂, R₃, R₄, R₅, R₇, R₉′, R₁₀, R₁₁, R_(P) and

are defined and described herein.

In embodiments in which R₁₀ is not hydrogen, the compound of formula (XII) may have the following structure:

wherein R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀′, R₁₁, R_(P) and

are defined and described herein.

In embodiments in which R₁₁ is not hydrogen, the compound of formula (XII) may have the following structure:

wherein R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁′, R_(P) and

are defined and described herein.

In certain embodiments,

is a polycyclic ring system such as a bicyclic or tricyclic moiety. In other embodiments,

is a monocyclic moiety. In yet other embodiments,

is a substituted or unsubstituted heterocyclic moiety. In other embodiments,

is a pyridinyl moiety as shown:

In another embodiment,

is selected from the group consisting of

In yet another embodiment,

is a five-membered heterocyclic ring selected from the group consisting of:

Various tetracyclines (heterocyclines) of the invention are also shown below:

wherein R₁, R₃, R₄, R₉, R₁₀, and R₁₁ are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁, are not simultaneously hydrogen.

Other compounds of the invention include pentacyclines of formula XIII, XIV, or XV:

or a pharmaceutically acceptable salt thereof; wherein the definitions of R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R_(P) and

are as defined above and described herein; and

R₁₂ is absent as valency permits; hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(D); —CH₂OR_(D); —CH₂R_(D); —CH₂N(R_(D))₂; ═C(R_(D))₂; ═O; —C(═O)R_(D); —CO₂R_(D); —CN; —SCN; —SR_(D); —SOR_(D); —SO₂R_(D); —N₃; —NO₂; —N(R_(D))₂; —NHC(O)R_(D); —NHSO₂R_(D); or —C(R_(D))₃; wherein each occurrence of R_(D) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In certain embodiments, one or more of the compounds of formula XIII, XIV and XV includes R₉′ in place of R₉; R₁₀′ in place of R₁₀; and/or R₁₁′ in place of R₁₁, wherein R₉′, R₁₀′, and R₁₁′ are as defined above and described herein.

In certain embodiments,

is a polycyclic ring system such as a bicyclic or tricyclic moiety. In other embodiments,

is a monocyclic moiety. In other embodiments,

is a substituted or unsubstituted, aromatic or nonaromatic carbocyclic moiety, for example a phenyl ring. In yet other embodiments,

is a substituted or unsubstituted heterocyclic moiety. In other embodiments,

is a pyridinyl moiety as shown:

In another embodiment,

is selected from the group consisting of

In yet another embodiment,

is a five-membered heterocyclic ring selected from the group consisting of

Various subclasses of the formula (XIII) include:

wherein R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R₁₂, R_(C) and

are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Various subclasses of the formula (XIV) include:

wherein R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R₁₂, R_(C) and

are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Various subclasses of the formula (XV) include:

wherein R₁, R₂, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R₁₂, R_(C) and

are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Various pentacyclines of the invention are shown below:

wherein R₁, R₃, R₄, R₉, R₁₀, and R₁₁ are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In certain embodiments, the tetracycline analogs of the present invention are represented by the formula (XVI):

or a pharmaceutically acceptable salt thereof; wherein

X is —N(R₁)—, —S—, or —O—;

represents a single or double bond;

R₃, R₄, R₅, R₆, R₇, R₈, R₉, R₁₀, R₁₁, and R_(P) are as defined above and described herein; and

n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In some embodiments, X is —N(R₁)—. In certain embodiments, X is —NH—. In other embodiments, X is —S— or —O—.

In certain embodiments, the compound of formula XVI includes R₉′ in place of R₉; R₁₀′ in place of R₁₀; and/or R₁₁′ in place of R₁₁, wherein R₉′, R₁₀′, and R₁₁′ are as defined above and described herein.

Subclasses of formula XVI, include:

wherein R₃, R₄, R₉, R₁₀, and R₁₁ are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Synthetic Methodology

The present invention provides all steps, methodologies, intermediates, and reagents useful in preparing an enone of formula (VII):

wherein R₃, R₄, R₅, R₉, R₁₀, R₁₁, and R_(P) are as defined above and described herein, provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

The present invention provides for use of this methodology in the modular synthesis of tetracycline analogs by joining the highly functionalized chiral enone, which will become the A- and B-rings of the tetracycline core, with a molecule which will become the D-ring of the tetracycline core. The joining of these two intermediates results in the formation of the C-ring, preferably in an enantioselective manner. This methodology also allows for the synthesis of pentacyclines, hexacyclines, or higher ring systems as well as the incorporation of heterocycles into the ring system. In particular, the joining of these two fragments includes various nucleophilic addition reactions and cycloaddition reactions with enone VII as described above and in published U.S. patent application US2005/0282787, published Dec. 22, 2005.

The synthesis of enone VII begins with an isoxazole of formula I. The isoxazole I is deprotonated by the addition of a suitable base and reacted with an enone of formula II to give the Michael adduct of formula III, wherein M is a counterion generated by the suitable base. The adduct of formula III is further treated, without work-up or purification, with a suitable base to effect a Claisen condensation yielding a compound of formula IV.

In some embodiments, the suitable base used to deprotonate I is a metal amide. In certain embodiments, the suitable base is a bis(trimethylsilyl)amide. In certain embodiments, the suitable base is sodium bis(trimethylsilyl)amide. In other embodiments, the base is lithium diisopropylamide or lithium diethylamide. In yet other embodiments, the base is sodium hydride or potassium hydride. In some embodiments, M is sodium, lithium, or potassium. In certain embodiments, M is sodium. In some embodiments, the reaction is performed a temperature from about −78° C. to about 0° C. In certain embodiments, the reaction is performed at −78° C. In certain other embodiments, the reaction is performed at −60° C. In yet other embodiments, the reaction is performed at −20° C. In some embodiments, the solvent used for the reaction is an aprotic solvent. In some embodiments, the solvent is a polar aprotic solvent. In certain embodiments, the solvent is an ether. In certain embodiments, the solvent is tetrahydrofuran. In some embodiments, the reaction further comprises an additive. In certain embodiments, the additive is hexamethylphosphoramide (HMPA). In certain other embodiments, the additive is 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU). In other embodiments, the additive is a copper-containing additive.

In certain embodiments, the Michael addition is stereoselective yielding only one or substantially one diastereomer. In certain embodiments, the diastereoselective reaction results in an diastereomeric excess (de) of at least 80%, at least 90%, at least 95%, at least 98%, or at least 99%. One of ordinary skill in the art would understand that the use of a compound of formula II having a different absolute or relative stereochemistry than that shown in the above Scheme in the Michael addition may produce compounds of other absolute or relative stereochemistry than that shown explicitly in the Scheme, and all of the possible enantiomers and diastereomers are encompassed by the present invention.

In some embodiments, each occurrence of R_(Q) is independently hydrogen, C₁₋₆ alkyl, —Si(OR_(Z))₃, or —Si(R_(Z))₃, wherein each occurrence of R_(Z) is independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; or a substituted or unsubstituted, branched or unbranched heteroaryl.

In some embodiments, R_(Q) is hydrogen. In other embodiments, R_(Q) is —Si(Me)₃. In other embodiments, R_(Q) is —Si(Me)₃. In yet other embodiments, R_(Q) is —SiH(Me)₂. In certain embodiments, R_(Q) is —SiH₂Me. In certain embodiments, R_(Q) is —Si(CH₃)₂(Ph). In yet other embodiments, R_(Q) is —Si(Et)₃. In certain embodiments, R_(Q) is —Si(iPr)₃. In certain embodiments, R_(Q) is —Si(Ph₂)_(t)Bu. In other embodiments, R_(Q) is —Si(tBu)(Me)₂. In certain embodiments, R_(Q) is —Si(Ph)₃. In certain embodiments, R_(Q) is —SiH(Ph)₂. In certain embodiments, R_(Q) is —SiH₂Ph. In other embodiments, R_(Q) is —SiH₃. In certain embodiments, R_(Q) is —Si(TMS)₃. In other embodiments, R_(Q) is —Si(OMe)₃. In yet other embodiments, R_(Q) is —SiH(OMe)₂. In certain embodiments, R_(Q) is —SiH₂OMe.

In some embodiments, the suitable base used to effect the Claisen condensation is an inorganic base. In other embodiments, the suitable base is an organic base. In some embodiments, the suitable base is a metal amide. In certain embodiments, the suitable base is a bis(trimethylsilyl)amide. In certain embodiments, the suitable base is potassium bis(trimethylsilyl)amide. In other embodiments, the base is lithium diisopropylamide or lithium diethylamide. In yet other embodiments, the base is sodium hydride or potassium hydride. In some embodiments, the reaction is performed at a temperature from about −78° C. to the refluxing temperature of the solvent. In certain embodiments, the reaction is performed at −78° C. In certain other embodiments, the reaction is performed at −20° C. In yet other embodiments, the reaction is performed at room temperature. In some embodiments, the solvent used for the reaction is an aprotic solvent. In some embodiments, the solvent is a polar aprotic solvent. In certain embodiments, the solvent is an ether. In certain embodiments, the solvent is tetrahydrofuran. In some embodiments, the reaction further comprises an additive. In certain embodiments, the additive is hexamethylphosphoramide (HMPA). In certain other embodiments, the additive is 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU). In other embodiments, the additive is a copper-containing additive.

A retro Diels-Alder reaction can be performed on the Michael-Claisen product of formula IV to give a compound of formula V. In some embodiments, the reaction is performed at an elevated temperature. In other embodiments, the reaction is performed at the reflux temperature of the solvent. In certain embodiments, the reaction is performed at about 250° C. In other embodiments, the reaction is performed at a temperature of less than about 250° C. or less than about 200° C., e.g., at a temperature of about 60° C., about 110° C., or about 170° C. In some embodiments, the solvent is a high boiling solvent. In certain embodiments, the solvent is diphenyl ether. In other embodiments, the solvent is toluent. In yet other embodiments, the solvent is hexafluoroisopropanol (HFIPA). In some embodiments, the reaction is run as a continuous-flow reaction. In certain embodiments, the continuous-flow reaction is aided by a setup as shown in FIG. 1. In some embodiments, a dienophile is present in the reaction mixture. In certain embodiments, dimethyl maleate is present in the reaction mixture. In certain other embodiments, dibutyl maleate is present in the reaction mixture. In yet other embodiments, maleic anhydride is present in the reaction mixture. In some embodiments, the continuous flow reaction can be performed using dienophile as solvent, e.g., dibutyl maleate.

In certain embodiments, the introduction of a silyl group at R_(Q) can make the retro Diels-Alder reaction more facile and may allow the reaction to proceed at a lower temperature and/or in higher yield. Examples include the following reactions:

In some embodiments, a retro Diels-Alder reaction yielding a compound of formula V may be followed by the reaction of this compound with a cyclopentadiene to yield an enone of formula II. The cyclopentadiene may be isolated and recycled under certain reaction conditions. An example of such a reaction includes the following:

A variety of cyclopentadienes may be reacted with a compound of formula V to yield an enone of formula II. In some instances, the cyclopentadiene may have the general formula:

wherein each occurrence of R_(Q) is independently hydrogen, C₁₋₆ alkyl, —Si(OR_(Z))₃, or —Si(R_(Z))₃, and wherein each occurrence of R_(Z) is independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; or a substituted or unsubstituted, branched or unbranched heteroaryl.

Examples of cyclopentadienes include the following:

A compound of formula V can be deprotonated with a suitable base and allowed to react with an electrophile to give an enone of formula VI. In some embodiments, the suitable base is a metal amide. In certain embodiments, the suitable base is a bis(trimethylsilyl)amide. In certain embodiments, the suitable base is lithium bis(trimethylsilyl)amide. In other embodiments, the base is lithium diethylamide or lithium diisopropylamide. In other embodiments, the base is a metal alkoxide. For example, in one embodiment, the base is lithium tert-butoxide. In yet other embodiments, the base is sodium hydride or potassium hydride. In some embodiments, the reaction is performed at a temperature from about −78° C. to room temperature. In certain embodiments, the reaction is performed at −78° C. In certain other embodiments, the reaction is performed at −30° C. In other embodiments, the reaction is performed at 0° C. In yet other embodiments, the reaction is performed at room temperature. In some embodiments, the solvent used for the reaction is an aprotic solvent. In some embodiments, the solvent is a polar aprotic solvent. In certain embodiments, the solvent is an ether. In certain embodiments, the solvent is dimethoxyethane. In some embodiments, the electrophile employed in the reaction results in a hydroxyl group in the product of formula VI. In some embodiments, the electrophile is trans-2-(phenylsulfonyl)-3-phenyloxaziridine, also known as Davis oxaziridine. In certain embodiments, the electrophile is trans-2-(phenylsulfonyl)-3-p-nitrophenyloxaziridine. In some embodiments, an inorganic salt is present in the reaction mixture. In certain embodiments, the inorganic salt, lithium chloride, is present in the reaction mixture. In some embodiments, the enone of formula VI is used in the next step without purification.

An exemplary synthetic scheme is as follows:

In certain embodiments, the electrophilic addition is stereoselective yielding only one or substantially one diastereomer. In certain embodiments, the diastereoselective reaction results in an diastereomeric excess (de) of at least 80%, at least 90%, at least 95%, at least 98%, or at least 99%. One of ordinary skill in the art would understand that the use of a compound of formula V with a different absolute or relative stereochemistry than that shown in the above scheme in the electrophilic addition may produce compounds of other absolute or relative stereochemistry than that shown explicitly in the scheme, and all of the possible enantiomers and diastereomers are encompassed by the present invention.

An enone of formula VI can be epimerized using a suitable acid to give an enone of formula VII. In some embodiments, the suitable acid is an inorganic acid. In certain embodiments, the suitable acid is sodium dihydrogenphosphate. In other embodiments, the suitable acid is potassium dihydrogenphosphate. In yet other embodiments, the suitable acid is sodium dihydrogenphosphate in aqueous hydrochloric acid. In some embodiments, the reaction mixture is biphasic. In some embodiments, an organic solvent is used in the reaction. In certain embodiments, the organic solvent is an ether. In certain other embodiments, the organic solvent is an alcohol. In certain embodiments, the solvent system comprises a mixture of an ether and an alcohol. In certain embodiments, the solvent system comprises methanol, tetrahydrofuran, and water. In some embodiments, the reaction takes place at a temperature between room temperature and the reflux temperature of the solvent. In certain embodiments, the reaction is performed at about 52° C.

In some embodiments, an enone of formula VI or VII can be further functionalized. In certain embodiments, when R₉ is —OH, the hydroxyl is optionally protected with a protecting group. In some embodiments, the protecting group is a silyl protecting group. In certain embodiments, the protecting group is a TBS group. In certain other embodiments, when R₉ is —OH, the hydroxyl group is optionally alkylated to form an alkoxy group. For example, the hydroxyl group can be treated with a base, e.g., lithium bis(trimethylsilyl)amide, optionally in the presence of an additive, e.g., HMPA, and reacted with an alkylating agent, e.g., methyl triflate to give a methoxy group.

In some embodiments, an enone of formula VI or VII is optionally functionalized such that R₁₀ is not hydrogen. For example, an enone of formula VI or VII can be treated with a suitable nucleophilic reagent in the presence of a suitable silylating reagent to effect a 1,4-conjugate addition to yield a silyl enol ether, which can then be treated with a suitable oxidant to generate the substituted enone. In some embodiments, the suitable nucleophilic reagent is an organometallic reagent. In some embodiments, the suitable nucleophilic reagent is an organocuprate. In certain embodiments, the suitable nucleophilic reagent is lithium dimethylcuprate. In some embodiments, the suitable silylating reagent is trimethylsilyl chloride. In certain embodiments, the suitable oxidant is palladium diacetate.

In some embodiments, an isoxazole of formula I′ is synthesized from an isoxazole of formula IX as shown below:

The compound of formula IX, wherein R₅ and R_(P) are as defined above and described herein, can be treated with a suitable base and reacted with phenylchloroformate to yield a compound of formula I′. In some embodiments, the suitable base is an organometallic base. In certain embodiments, the suitable base is butyllithium. In certain embodiments, the suitable base is n-butyllithium.

In some embodiments, an enone of formula II, wherein R₁₁ is not hydrogen, is synthesized from an enone of formula II-H wherein R₁₁ is hydrogen as shown below:

An enone of formula II-H can be treated with a suitable nucleophilic reagent in the presence of a suitable silylating reagent to effect a 1,4-conjugate addition to yield a silyl enol ether of formula X, wherein R₁₅ is a C₁₋₆ alkyl group, which can then be treated with a suitable oxidant to generate the substituted enone of formula II, wherein R₁₁ is not hydrogen. In some embodiments, the suitable nucleophilic reagent is an organometallic reagent. In some embodiments, the suitable nucleophilic reagent is an organocuprate. In certain embodiments, the suitable nucleophilic reagent is lithium dimethylcuprate. In some embodiments, the suitable silylating reagent is trimethylsilyl chloride. In certain embodiments, the suitable oxidant is palladium diacetate. In certain embodiments, an enone of formula II-H can be synthesized as shown below:

where each occurrence of R_(Q) is independently hydrogen, C₁₋₆ alkyl, —Si(OR_(Z))₃, or —Si(R_(Z))₃, wherein each occurrence of R_(Z) is independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; or a substituted or unsubstituted, branched or unbranched heteroaryl.

In some embodiments, a compound of formula I′ and a compound of formula II′ are subjected to Michael-Claisen conditions as described herein to yield a compound of formula IV′.

In some embodiments, the suitable base used to deprotonate I′ is a metal amide. In certain embodiments, the suitable base is a bis(trimethylsilyl)amide. In certain embodiments, the suitable base is lithium bis(trimethylsilyl)amide. In other embodiments, the base is lithium diisopropylamide or lithium diethylamide. In yet other embodiments, the base is sodium hydride or potassium hydride. In some embodiments, M is sodium, lithium, or potassium. In certain embodiments, M is lithium. In some embodiments, the reaction is performed a temperature from about −78° C. to about 0° C. In certain embodiments, the reaction is performed at −78° C. In certain other embodiments, the reaction is performed at −60° C. In yet other embodiments, the reaction is performed at −20° C. In some embodiments, the solvent used for the reaction is an aprotic solvent. In some embodiments, the solvent is a polar aprotic solvent. In certain embodiments, the solvent is an ether. In certain embodiments, the solvent is tetrahydrofuran. In some embodiments, the reaction further comprises an additive. In certain embodiments, the additive is hexamethylphosphoramide (HMPA). In certain other embodiments, the additive is 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU). In other embodiments, the additive is a copper-containing additive.

In certain embodiments, the Michael addition is stereoselective yielding only one or substantially one diastereomer. In certain embodiments, the diastereoselective reaction results in an diastereomeric excess (de) of at least 80%, at least 90%, at least 95%, at least 98%, or at least 99%. One of ordinary skill in the art would understand that the use of a compound of formula II′ with a different absolute or relative stereochemistry than that shown in the above scheme in the Michael addition may produce compounds of other absolute or relative stereochemistry than that shown explicitly in the scheme, and all of the possible enantiomers and diastereomers are contemplated by the present invention.

In some embodiments, the suitable base used to effect the Claisen condensation is an inorganic base. In other embodiments, the suitable base is an organic base. In some embodiments, the suitable base is a metal amide. In certain embodiments, the suitable base is a bis(trimethylsilyl)amide. In certain embodiments, the suitable base is potassium bis(trimethylsilyl)amide. In other embodiments, the base is lithium diisopropylamide or lithium diethylamide. In yet other embodiments, the base is sodium hydride or potassium hydride. In some embodiments, the reaction is performed at a temperature from about −78° C. to the refluxing temperature of the solvent. In certain embodiments, the reaction is performed at −78° C. In certain other embodiments, the reaction is performed at −20° C. In yet other embodiments, the reaction is performed at room temperature. In some embodiments, the solvent used for the reaction is an aprotic solvent. In some embodiments, the solvent is a polar aprotic solvent. In certain embodiments, the solvent is an ether. In certain embodiments, the solvent is tetrahydrofuran. In some embodiments, the reaction further comprises an additive. In certain embodiments, the additive is hexamethylphosphoramide (RMPA). In certain other embodiments, the additive is 1,3-dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone (DMPU). In other embodiments, the additive is a copper-containing additive.

In some embodiments, when R₉ is alkyl, the compound of formula IIa is prepared as shown below:

An allylic displacement reaction is performed on the allylic acetate using an organometallic reagent. In some embodiments, the organometallic reagent is an organocuprate. In certain embodiments, the organometallic reagent is an alkyllithium reagent and copper cyanide. In certain embodiments, the alkyllithium reagent is methyllithium. The resulting alcohol is oxidized to the ketone using an oxidant. In some embodiments, the oxidant is IBX. The resulting ketone is treated with a base to give the enone of formula IIa, wherein R₉ is alkyl. In some embodiments, the base is an alkoxide. In certain embodiments, the base is methoxide. In certain embodiments, the base is sodium methoxide in methanol.

The compound of formula IIa can then be used to synthesize a compound of formula VIIa, as shown below:

The isoxazole I is deprotonated by the addition of a suitable base and reacted with an enone of formula IIa to give the Michael-Claisen product of formula IVa. In some embodiments, the suitable base used to deprotonate I is a metal amide. In certain embodiments, the suitable base is a bis(trimethylsilyl)amide. In certain embodiments, the suitable base is sodium bis(trimethylsilyl)amide. In some embodiments, the suitable base is lithium bis(trimethylsilyl)amide. In certain embodiments, the Michael addition/Claisen condensation is stereoselective yielding only one or substantially one enantiomer. In certain embodiments, the enantioselective reaction results in an enantiomeric excess (ee) of at least 80%, at least 90%, at least 95%, at least 98%, or at least 99%. One of ordinary skill in the art would understand that the use of a compound of formula IIa having a different absolute or relative stereochemistry than that shown in the above scheme in the Michael addition may produce compounds of other absolute or relative stereochemistry than that shown explicitly in the scheme, and all of the possible enantiomers and diastereomers are encompassed by the present invention.

A retro Diels-Alder reaction can be performed on the Michael-Claisen product of formula IVa to give an enone of formula VIa. In some embodiments, the reaction is performed at an elevated temperature. In other embodiments, the reaction is performed at the reflux temperature of the solvent. In certain embodiments, the reaction is performed at about 250° C. In some embodiments, the solvent is a high boiling solvent. In certain embodiments, the solvent is diphenyl ether. In some embodiments, the reaction is run as a continuous-flow reaction. In certain embodiments, the continuous-flow reaction is aided by a setup as described in FIG. 1. In some embodiments, a dienophile is present in the reaction mixture. In certain embodiments, dimethyl maleate is present in the reaction mixture. In other embodiments, dibutyl maleate is present in the reaction mixture. In yet other embodiments, maleic anhydride is present in the reaction mixture. In some embodiments, the continuous flow reaction is performed using the dienophile as solvent, e.g., dibutyl maleate.

An enone of formula VIa can be epimerized using a suitable acid to give an enone of formula VIIa. In some embodiments, the suitable acid is an inorganic acid. In certain embodiments, the suitable acid is sodium dihydrogenphosphate. In other embodiments, the suitable acid is potassium dihydrogenphosphate. In yet other embodiments, the suitable acid is sodium dihydrogenphosphate in aqueous hydrochloric acid. In some embodiments, the reaction mixture is biphasic. In some embodiments, an organic solvent is used in the reaction. In certain embodiments, the organic solvent is an ether. In certain other embodiments, the organic solvent is an alcohol. In certain embodiments, the solvent system comprises a mixture of an ether and an alcohol. In certain embodiments, the solvent system comprises methanol, tetrahydrofuran, and water. In some embodiments, the reaction takes place at a temperature between room temperature and the reflux temperature of the solvent. In certain embodiments, the reaction is performed at a temperature ranging from about 40° C. to about 60° C. In certain embodiments, the reaction is performed at a temperature ranging from about 45° C. to about 55° C. In certain embodiments, the reaction is performed at about 52° C.

In some embodiments, an enone of formula VIIa or VIIa is optionally functionalized such that R₁₀ is not hydrogen. For example, an enone of formula VIa or VIIa can be treated with a suitable nucleophilic reagent in the presence of a suitable silylating reagent to effect a 1,4-conjugate addition to yield a silyl enol ether, which can then be treated with a suitable oxidant to generate the substituted enone. In some embodiments, the suitable nucleophilic reagent is an organometallic reagent. In some embodiments, the suitable nucleophilic reagent is an organocuprate. In certain embodiments, the suitable nucleophilic reagent is lithium dimethylcuprate. In some embodiments, the suitable silylating reagent is trimethylsilyl chloride. In certain embodiments, the suitable oxidant is palladium diacetate.

In another aspect, an enone of formula VII may be functionalized at the C5 position by employing a bromination/nucleophilic displacement sequence. An exemplary scheme is shown below. The enone can be protected with a silyl protecting group, e.g., trimethylsilyl, triisopropylsilyl, tert-butyldimethylsilyl, by treating with a silylating reagent, e.g., trimethylsilyl triflate, triisopropylsilyl triflate, tert-butyldimethylsilyl triflate, then treated with a brominating agent, e.g., N-bromosuccinimide, to yield the enone having a bromine at the C5 position. The bromine can then be displaced with a variety of reagents, e.g., tetramethylguanidinium azide, to yield the desired functionality at C5, e.g., azide. Further transformations can be performed if desired to yield other functionalities, e.g., amino.

As would be appreciated by one of skill in the art, each of the steps in the synthesis of the enone may be optionally followed by the appropriate work-up and purification of the desired product. Certain steps, however, may not require purification before being used as starting material in the next reaction. The inventive synthesis of the enone may be used to prepare multi-gram quantities. In certain embodiments, at least 25 grams of the enone is prepared. In other embodiments, at least 50 grams of the enone is prepared using the inventive synthesis. In certain other embodiments, at least 100 grams of the enone is prepared. In certain embodiments, the enone is prepared on a kilogram scale or greater.

In some embodiments, an enone of formula VII may be functionalized at the C5 position by reaction with a cation. An exemplary scheme is shown below. The enone can be protected with a silyl or other protecting group, such as those described herein.

The enone VII is then optionally reacted with anion of a phthalide, an anion of a toluate, a benzocyclobutenole, or a diene to yield a tetracycline analog. Details of these reactions and possible phthalides, toluates, benzocyclobutenoles, and dienes are described in U.S. patent application US 2005/0282787, published Dec. 22, 2005; WO 05/112945, published on Dec. 1, 2005; and U.S. provisional patent application, U.S. Ser. No. 60/790,413, filed Apr. 7, 2006. Exemplary schemes are shown below.

In one embodiment, an enone of formula VII is reacted with a protecting group at the C5a position, and the reaction product is reacted with a toluate to yield a tetracycline analog. An exemplary scheme is shown below:

Another exemplary scheme for reacting an enone of formula VII with a protecting group at the C5a position, and then reacting the reaction product with a toluate to yield a tetracycline analog, is shown below:

In one embodiment, an enone of formula VII is reacted with anion resulting from the deprotonation of a toluate of formula:

wherein R₁, R₇ and R_(P) are as defined above and described herein;

n is an integer in the range of 0 to 3, inclusive;

R₁₃ is —OR_(E), —CN, —SCN, —SR_(E), or —N(R_(E))₂; wherein each R_(E) is independently hydrogen; a protecting group; a cyclic or acyclic, substituted or unsubstituted aliphatic; a cyclic or acyclic, substituted or unsubstituted heteroaliphatic; a substituted or unsubstituted aryl; or a substituted or unsubstituted heteroaryl;

is deprotonated under basic conditions (e.g., LDA, HMDS), and the resulting anion is reacted with an enone of formula:

wherein R₃, R₄, R₅, R₉, R₁₀, R₁₁, and R_(P) are as defined above and described herein, provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen; to form the product:

wherein R₁, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R_(P), and n are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

As will be appreciated by one of skill in this art, the toluate may be further substituted in certain embodiments. In addition, the phenyl ring of the toluate may be substituted for an aromatic heterocyclic ring such as a pyridine ring. Other examples of carbocyclic and heterocyclic toluate analogs include:

In certain embodiments, polycyclic toluates are used in the Michael-Dieckmann reaction sequence to form pentacyclines, hexacyclines, or higher cyclines. Toluates useful in preparing pentacyclines are exemplified by the formula:

wherein R₁, R₇, R₁₃, R_(P), and

are as defined above and described herein.

In another embodiment, an enone of formula VII is reacted with anion, which is generated through metalation (e.g., metal-halogen exchange, metal-metalloid exchange, lithium-halogen exchange, lithium-tin exchange, etc. by reacting the toluate with the appropriate metal reagent) of a toluate of the following formula:

wherein

R₁ and R₇ are as defined above and described herein;

n is an integer in the range of 0 to 3, inclusive;

R₁₄ is selected from the group consisting of substituted or unsubstituted aryl or heteroaryl groups; and

Y is hydrogen, a halogen or Sn(R_(Y))₃, wherein R_(Y) is alkyl. The anion generated is reacted with the enone (VII) to generate a product of formula:

wherein R₁, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R_(P), and n are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

Any metal may be used in the metalation reaction to generate the metal anionic reagent to be reacted with the enone. In certain embodiments, the metal is a Group I element on the periodic chart. In other embodiments, the metal is a Group II element on the periodic chart. In other embodiments, the metal is a transition metal. Exemplary metals useful in the metalation reaction include sodium, lithium, calcium, aluminium, cadmium, copper, beryllium, arsenic, antimony, tin, magnesium, titanium, zinc, manganese, iron, cobalt, nickel, zinc, platinum, palladium, mercury, and ruthenium. In certain preferred embodiments, the metal is chosen from lithium, magnesium, titanium, zinc, and copper. In yet other embodiments, the metal is magnesium, lithium, sodium, beryllium, zinc, mercury, arsenic, antimony, or tin. In certain particular embodiments, a lithium-halogen exchange is used. The lithium-halogen exchange may be performed in situ in the presence of the enone. The lithium-halogen exchange may be preformed using any lithium reagent including, for example, alkyllithium reagents, n-butyllithium, t-butyllithium, phenyl lithium, mesityl lithium, and methyllithium. In certain embodiments, other organometallics reagents are generated and reacted with the enone. Examples include Grignard reagents, zero-valent metal complexes, ate complexes, etc. In certain embodiments, the metal reagent is a magnesium reagent including, but not limited to, magnesium metal, magnesium anthracene, activated magnesium turnings, etc. In certain embodiments, the reagent is zinc-based. The reagent may be generated in situ in the presence of the enone, or the reagent may be generated separately and later contacted with the enone. In certain embodiments, milder conditions for the cyclization are used (e.g., a zinc reagent).

As will be appreciated by one of skill in this art, the toluate may be further substituted in certain embodiments. In addition, the phenyl ring of the toluate may be substituted for an aromatic heterocyclic ring or ring system such as a pyridine ring. Examples of carbocyclic and heterocyclic analogs of toluate include:

In certain embodiments, the halogen Y is bromine. In other embodiments, Y is iodine. In yet other embodiments, Y is chloride. In some embodiments, Y is hydrogen. In certain embodiments, Y is a metalloid (e.g., tin, selenium, tellurium, etc.). In certain embodiments, Y is —SnR₃, wherein each occurrence of R is independently alkyl (e.g., —Sn(CH₃)₃). After the metalation reaction, Y is a metal such as lithium, magnesium, zinc, copper, antimony, sodium, etc. In certain embodiments, R₁ is hydrogen or C₁₋₆ alkyl. In certain particular embodiments, R₁ is hydrogen.

In other embodiments, polycyclic toluates may be used to prepare pentacyclines, hexacyclines, or higher cyclines. Toluates useful in the preparation of such cyclines are of the formula:

wherein R₁, and R₇ are as defined above and described herein; n is an integer in the range of 0 to 3, inclusive;

R₁₄ is selected from the group consisting of substituted or unsubstituted aryl or heteroaryl groups;

represents a substituted or unsubstituted aryl, heteroaryl, carbocyclic, or heterocyclic moiety, in which each occurrence of X is independently —O—, —S—, —NR₁₂—, or —C(R₁₂)₂—; n is an integer in the range of 1 to 5, inclusive; and the bonds between adjacent X moieties are either single or double bonds;

R₁₂ is as defined above and described herein; and

Y is hydrogen, a halogen or Sn(R_(Y))₃, wherein R_(Y) is alkyl.

In certain embodiments, the halogen Y is bromine. In certain embodiments, the halogen Y is bromine. In other embodiments, Y is iodine. In yet other embodiments, Y is chloride. In some embodiments, Y is hydrogen. In certain embodiments, Y is a metalloid (e.g., tin, selenium, tellurium, etc.). In certain embodiments, Y is —SnR₃, wherein each occurrence of R is independently alkyl (e.g., —Sn(CH₃)₃). After the metalation reaction, Y is a metal such as lithium, magnesium, zinc, copper, sodium, mercury, antimony, etc. In certain embodiments, R₁ is hydrogen or C₁₋₆ alkyl. In certain particular embodiments, R₁ is hydrogen. In certain embodiments, R₁₄ is phenyl or substituted phenyl. In certain embodiments, ortho-R₇ is alkoxy such as methoxy. In other embodiments, R₇ is hydrogen. Exemplary polycyclic toluates include:

Compounds of the formula below with a heterocyclic C-ring:

may be prepared by Michael-Dieckmann closure of a D-ring precursor derived from the corresponding anilide, phenol, or thiophenol. A representative example using anthranilic acid (i.e., anilide as the nucleophile in the Michael addition reaction) is shown below:

In another embodiment, the enone of formula VII is reacted with a benzocyclobutenol in an o-quinone dimethide Diels-Alder reaction. The enone VII is reacted under suitable conditions (e.g., heat) with a benzocyclobutenol of formula:

wherein R₁, R₇ and R_(P) are as defined above and described herein;

n is an integer in the range of 0 to 3, inclusive;

to form the product of formula:

wherein R₁, R₃, R₄, R₅, R₆, R₇, R₉, R₁₀, R₁₁, and R_(P) are defined as above; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen. As will be appreciate by one of skill in this art, the reactants may be substituted further and still fall within the claimed invention. For example, the phenyl ring of the benzocyclobutenol ring may be further substituted.

In another embodiment, the enone is reacted with a diene in a Diels-Alder reaction to yield a tricycline. The enone VII is reacted under suitable conditions (e.g., heat) with a diene of formula:

wherein R₁ and R_(P) are as defined above and described herein;

to yield a protected tricycline of formula:

wherein R₁, R₃, R₄, R₅, R₆, R₉, R₁₀, R₁₁, and R_(P) are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen. As will be appreciated by one of skill in this art, the enone and diene may be further substituted and still be encompassed within the present invention.

In yet another embodiment, the enone is reacted with anion of a phthalide or cyano-phthalide. The enone of formula VII is reacted under basic conditions (e.g., LDA, Ph₃CLi) with the anion of the phthalide of formula:

wherein R₁, R₇, and R_(P) are as defined above and described herein; and

n is an integer in the range of 0 to 3, inclusive;

to yield a product of formula:

wherein R₁, R₃, R₄, R₅, R₇, R₉, R₁₀, R₁₁, R_(P), and n are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

The products of the above reactions are optionally further functionalized, reduced, oxidized, rearranged, protected, and deprotected to yield the final desired product. Each of the above steps may be followed with an appropriate work-up and purification of the desired product. As will be appreciated by one of skill in the art, various isolation and purification techniques including flash chromatography, crystallization, distillation, HPLC, thin layer chromatography, extraction, filtration, etc. may be used in the course of synthesizing compounds of the invention. These techniques may be used in the preparation or purification of intermediates, reagents, products, starting materials, or solvents.

As an example of a further reaction of a tetracycline, the formula:

wherein R₁, R₃, R₄, R₅, R₇, R₉, R₁₁, and R_(P) are as defined above and described herein and n is an integer in the range of 0 to 8, inclusive, can be reacted with carbonyl dichloride to yield a cyclopropane intermediate of formula:

The cyclopropane intermediate can be reacted with a variety of nucleophiles (e.g., —CN, —OCH₃, —OCHOCH₃, morpholine, piperidine, tert-butyl 1-peperazine carboxylate, cyclopropylamine, diethylamine, 2-(methylamino)ethanol, 3-dimethylamino-1-propylamine, 2-methoxyethanol, imidazole, 3-aminopyridine) to yield a desired structure having the formula:

wherein R_(N) is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —OCHOR_(C); —CH₂OR_(C); —CH₂R_(C); —OCH₂CH₂N(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio.

An exemplary scheme for preparing and modifying a cyclopropane intermediate is shown below:

The cyclopropane chemistry may be applied to a variety of tetracycline analogs as described herein.

In certain embodiments, modification of a cycloproprane intermediate may yield a tetracycline having an aminomethyl group at the C5a position. The tetracycline analog may be further reacted, e.g., with an acyl chloride or anhydride, to generate a variety of tetracycline analogs as described herein.

Intermediates

Along with synthetic methodology, the invention also provides useful intermediates useful in the preparation of the enone of formula VII and tetracycline analogs.

In certain embodiments, the invention provides a compound of formula (VII):

wherein R₃, R₄, R₅, R₉, R₁₀, R₁₁, R_(P) and n are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In some embodiments, R₃ is hydrogen, halogen, —OR_(B), or C₁₋₆ alkyl. In other embodiments, R₃ is —OR_(B). In certain embodiments, R₃ is hydroxyl. In certain other embodiments, R₃ is fluorine. In yet other embodiments, R₃ is hydrogen. In some embodiments, R₄ is hydrogen, halogen, —OR_(B), or C₁₋₆ alkyl. In other embodiments, R₄ is —OR_(B). In certain embodiments, R₄ is hydroxy. In certain other embodiments, R₄ is fluorine. In yet other embodiments, R₄ is hydrogen. In some embodiments, R₃ is —N(R_(B))₂. In other embodiments, R₄ is —N(R_(B))₂. In certain embodiments, R₃ is —NHC(O)R_(B) or —NHSO₂R_(B). In certain other embodiments, R₄ is —NHC(O)R_(B) or —NHSO₂R_(B). In certain embodiments, R₃ and R₄ are both hydrogen. In some embodiments, R₃ is —OR_(B), and R₄ is hydrogen. In other embodiments, R₃ is hydrogen, and R₄ is —OR_(B). In certain embodiments, R₃ is hydroxyl, and R₄ is hydrogen. In certain other embodiments, R₃ is hydrogen, and R₄ is hydroxyl. In some embodiments, R₃ is fluorine, and R₄ is hydrogen. In other embodiments, R₃ is hydrogen, and R₄ is fluorine. In certain embodiments, R₃ and R₄ are both fluorine.

In some embodiments, R₅ is —N(R_(C))₂. In certain embodiments, R₅ is —N(R_(C))₂, wherein R_(C) is hydrogen or C₁₋₆ alkyl. In certain other embodiments, R₅ is —N(R_(E))₂, wherein R_(E) is methyl. In some embodiments, R₅ is —OR_(C) or —SR_(C). In other embodiments, R₅ is substituted or unsubstituted aliphatic. In yet other embodiments, R₅ is substituted or unsubstituted heteroaliphatic. In certain embodiments, R₅ is C₁₋₆ alkyl. In certain other embodiments, R₅ is hydrogen.

In some embodiments, R₉ is —OR_(C). In certain embodiments, R₉ is hydroxyl. In certain other embodiments, R₉ is methoxy. In some embodiments, R₉ is —OC(R_(C))₃, wherein at least one R_(C) is a halogen. In certain embodiments, R₉ is —OCF₃, OCHF₂, or OCH₂F. In some embodiments, R₉ is —CH₂R_(C), where R_(C) is a halogen. In certain embodiments, R₉ is —CH₂OH, In certain embodiments, R₉ is —CH₂OCH₃. In certain embodiments, R₉ is —CH₂N₃. In some embodiments, R₉ is —C(═O)R_(C). In other embodiments, R₉ is —COOR_(C). In some embodiments, R₉ is —C(═O)NR_(C). In some embodiments, R₉ is —CH₂SH. In other embodiments, R₉ is —CH₂SCH₃. In some embodiments, R₉ is alkoxy. In certain embodiments, R₉ is —OR_(C). In certain embodiments, R₉ is ethoxy. In certain embodiments, R₉ is propoxy. In certain embodiments, R₉ is butoxy. In some embodiments, R₉ is —SR_(C). In some embodiments, R₉ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₉ is alkylthiol. In certain embodiments, R₉ is C₁₋₆ alkylthiol. In certain embodiments, R₉ is methanethiol. In certain embodiments, R₉ is ethanethiol. In certain embodiments, R₉ is propanethiol. In certain embodiments, R₉ is butanethiol. In certain embodiments, R₉ is thiol. In certain embodiments, R₉ is hydrogen. In some embodiments, R₉ is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic. In some embodiments, R₉ is alkyl. In some embodiments, R₉ is C₁₋₆ alkyl. In certain embodiments, R₉ is methyl. In certain embodiments, R₉ is ethyl. In certain embodiments, R₉ is propyl. In certain embodiments, R₉ is butyl. In some embodiments, R₉ is halogen. In certain embodiments, R₉ is fluorine. In other embodiments, R₉ is —N(R_(C))₂ or —NH(R_(C)). In certain embodiments, R₉ is alkylamino or dialkylamino. In some embodiments, R₉ is a protected hydroxyl group. In certain embodiments, the R₉ hydroxyl group is protected with a silyl-protecting group. In certain embodiments, R₉ is —OTBS. In some embodiments, R₉ is a fluoroalkyl group. In certain embodiments, R₉ is —CF₃, —CHF₂, or —CH₂F.

In some embodiments, R₁₀ is substituted or unsubstituted alkyl. In other embodiments, R₁₀ is —OR_(C). In some embodiments, R₁₀ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In certain embodiments, R₁₀ is alkoxy. In certain embodiments, R₁₀ is C₁₋₆ alkoxy. In certain embodiments, R₁₀ is —CH₂OH, In certain embodiments, R₁₀ is —CH₂OCH₃. In certain embodiments, R₁₀ is —CH₂N₃. In certain embodiments, R₁₀ is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, R₁₀ is —N(R_(C))₂. In some embodiments, R₁₀ is —SR_(C). In some embodiments, R₁₀ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₁₀ is alkylthiol. In certain embodiments, R₁₀ is C₁₋₆ alkylthiol. In certain embodiments, R₁₀ is methanethiol. In certain embodiments, R₁₀ is ethanethiol. In certain embodiments, R₁₀ is propanethiol. In certain embodiments, R₁₀ is butanethiol. In certain embodiments, R₁₀ is thiol. In certain embodiments, R₁₀ is hydroxyl. In certain embodiments, R₁₀ is halogen. In other embodiments, R₁₀ is fluorine. In some embodiments, R₁₀ is C₁₋₆ alkyl. In certain embodiments, R₁₀ is methyl. In certain embodiments, R₁₀ is ethyl In certain embodiments, R₁₀ is propyl. In certain embodiments, R₁₀ is butyl. In certain other embodiments, R₁₀ is —CF₃, —CHF₂, or —CH₂F. In certain embodiments, R₁₀ is hydrogen. In other embodiments, R₁₀ is not hydrogen.

In certain embodiments, R₁₁ is substituted or unsubstituted aliphatic. In some embodiments, R₁₁ is substituted or unsubstituted alkyl. In other embodiments, R₁₁ is —OR_(C). In yet other embodiments, R₁₁ is —N(R_(C))₂. In other embodiments, R₁₁ is —OR_(C). In some embodiments, R₁₁ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In certain embodiments, R₁₁ is alkoxy. In certain embodiments, R₁₁ is C₁₋₆ alkoxy. In certain embodiments, R₁₁ is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, R₁₁ is —SR_(C). In some embodiments, R₁₁ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₁₁ is alkylthiol. In certain embodiments, R₁₁ is C₁₋₆ alkylthiol. In certain embodiments, R₁₁ is methanethiol. In certain embodiments, R₁₁ is ethanethiol. In certain embodiments, R₁₁ is propanethiol. In certain embodiments, R₁₁ is butanethiol. In certain embodiments, R₁₁ is thiol. In certain embodiments, R₁₁ is hydroxyl, methoxy, or trifluoromethoxy. In certain embodiments, R₁₁ is hydroxyl. In certain embodiments, R₁₁ is halogen. In other embodiments, R₁₁ is fluorine. In some embodiments, R₁₁ is C₁₋₆ alkyl. In certain embodiments, R₁₁ is methyl. In certain embodiments, R₁₁ is ethyl. In certain embodiments, R₁₁ is propyl. In certain embodiments, R₁₁ is butyl. In certain other embodiments, R₁₃ is —CF₃, —CHF₂, or —CH₂F. In certain embodiments, R₁₁ is hydrogen. In other embodiments, R₁₁ is not hydrogen.

In certain embodiments, R_(P) is benzyl. In other embodiments, R_(P) is hydrogen. In yet other embodiments, R_(P) is acyl. In yet other embodiments, R_(P) is a silicon-containing protecting group.

As described above, in certain embodiments, the compounds of formula VII includes R₉′ in place of R₉; R₁₀′ in place of R₁₀; and/or R₁₁′ in place of R₁₁, wherein R₉′, R₁₀′, and R₁₁′ are as defined above and described herein.

In certain embodiments, a compound of formula VII has one of the following formulae:

Exemplary compounds of formula VII include:

In certain embodiments, the invention provides a compound of formula (VI):

wherein R₃, R₄, R₅, R₉, R₁₀, R₁₁, and R_(P) are as defined above and described herein; provided that when R₉ is —OR_(C), R₁₀ and R₁₁ are not simultaneously hydrogen.

In certain embodiments, the compound of formula VI includes R₉′ in place of R₉; R₁₀′ in place of R₁₀; and/or R₁₁′ in place of R₁₁, wherein R₉′, R₁₀′, and R₁₁′ are as defined above and described herein.

In some embodiments, R₁₀ is not hydrogen. In some embodiments, R₁₁ is not hydrogen. In some embodiments, at least one of R₁₀ and R₁₁ is not hydrogen. In some embodiments, both R₁₀ and R₁₁ are not hydrogen.

In some embodiments, R₉ is not —OR_(C). In some embodiments, R₉ is not —OR_(C) when both R₁₀ and R₁₁ are hydrogen. In some embodiments, R₉ is not —OR_(C), wherein R_(C) is hydrogen or an oxygen-protecting group. In certain embodiments, R₉ is not —OH. In other embodiments, when R₉ is —OR_(C), the substituents at R₁₀ and R₁₁ are not simultaneously hydrogen, and R₃ and R₄ are not hydrogen or —OR_(B). In some embodiments, when R₉ is not hydroxyl or a protected hydroxyl, R₁₀ and R₁₁ may be simultaneously hydrogen.

In some embodiments, R₃ is hydrogen, halogen, —OR_(B), or C₁₋₆ alkyl. In other embodiments, R₃ is —OR_(B). In certain embodiments, R₃ is hydroxyl. In certain other embodiments, R₃ is fluorine. In yet other embodiments, R₃ is hydrogen. In some embodiments, R₄ is hydrogen, halogen, —OR_(B), or C₁₋₆ alkyl. In other embodiments, R₄ is —OR_(B). In certain embodiments, R₄ is hydroxy. In certain other embodiments, R₄ is fluorine. In yet other embodiments, R₄ is hydrogen. In some embodiments, R₃ is —N(R_(B))₂. In other embodiments, R₄ is —N(R_(B))₂. In certain embodiments, R₃ is —NHC(O)R_(B) or —NHSO₂R_(B). In certain other embodiments, R₄ is —NHC(O)R_(B) or —NHSO₂R_(B). In certain embodiments, R₃ and R₄ are both hydrogen. In some embodiments, R₃ is —OR_(B), and R₄ is hydrogen. In other embodiments, R₃ is hydrogen, and R₄ is —OR_(B). In certain embodiments, R₃ is hydroxyl, and R₄ is hydrogen. In certain other embodiments, R₃ is hydrogen, and R₄ is hydroxyl. In some embodiments, R₃ is fluorine, and R₄ is hydrogen. In other embodiments, R₃ is hydrogen, and R₄ is fluorine. In certain embodiments, R₃ and R₄ are both fluorine.

In some embodiments, R₅ is —N(R_(C))₂. In certain embodiments, R₅ is —N(R_(C))₂, wherein R_(C) is hydrogen or C₁₋₆ alkyl. In certain other embodiments, R₅ is —N(R_(E))₂, wherein R_(E) is methyl. In some embodiments, R₅ is —OR_(C) or —SR_(C). In other embodiments, R₅ is substituted or unsubstituted aliphatic. In yet other embodiments, R₅ is substituted or unsubstituted heteroaliphatic. In certain embodiments, R₅ is C₁₋₆ alkyl. In certain other embodiments, R₅ is hydrogen.

In some embodiments, R₉ is —OR_(C). In certain embodiments, R₉ is hydroxyl. In certain other embodiments, R₉ is methoxy. In some embodiments, R₉ is alkoxy. In certain embodiments, R₉ is —OR_(C). In some embodiments, R₉ is —OC(R_(C))₃, wherein at least one R_(C) is a halogen. In certain embodiments, R₉ is —OCF₃, —OCHF₂, or —OCH₂F. In certain embodiments, R₉ is ethoxy. In certain embodiments, R₉ is propoxy. In certain embodiments, R₉ is butoxy. In some embodiments, R₉ is —SR_(C). In some embodiments, R₉ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₉ is alkylthiol. In certain embodiments, R₉ is C₁₋₆ alkylthiol. In certain embodiments, R₉ is methanethiol. In certain embodiments, R₉ is ethanethiol. In certain embodiments, R₉ is propanethiol. In certain embodiments, R₉ is butanethiol. In certain embodiments, R₉ is thiol. In certain embodiments, R₉ is hydrogen. In some embodiments, R₉ is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic. In some embodiments, R₉ is alkyl. In some embodiments, R₉ is C₁₋₆ alkyl. In certain embodiments, R₉ is methyl. In certain embodiments, R₉ is ethyl. In certain embodiments, R₉ is propyl. In certain embodiments, R₉ is butyl. In some embodiments, R₉ is halogen. In certain embodiments, R₉ is fluorine. In other embodiments, R₉ is —N(R_(C))₂ or —NH(R_(C)). In certain embodiments, R₉ is alkylamino or dialkylamino. In some embodiments, R₉ is a protected hydroxyl group. In certain embodiments, the R₉ hydroxyl group is protected with a silyl-protecting group. In certain embodiments, R₉ is —OTBS. In some embodiments, R₉ is a fluoroalkyl group. In certain embodiments, R₉ is —CF₃, —CHF₂, or —CH₂F.

In some embodiments, R₁₀ is substituted or unsubstituted alkyl. In other embodiments, R₁₀ is —OR_(C). In some embodiments, R₁₀ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In certain embodiments, R₁₀ is alkoxy. In certain embodiments, R₁₀ is C₁₋₆ alkoxy. In certain embodiments, R₁₀ is —CH₂OH, In certain embodiments, R₁₀ is —CH₂OCH₃. In certain embodiments, R₁₀ is —CH₂N₃. In certain embodiments, R₁₀ is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, R₁₀ is —N(R_(C))₂. In some embodiments, R₁₀ is —SR_(C). In some embodiments, R₁₀ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₁₀ is alkylthiol. In certain embodiments, R₁₀ is C₁₋₆ alkylthiol. In certain embodiments, R₁₀ is methanethiol. In certain embodiments, R₁₀ is ethanethiol. In certain embodiments, R₁₀ is propanethiol. In certain embodiments, R₁₀ is butanethiol. In certain embodiments, R₁₀ is thiol. In certain embodiments, R₁₀ is hydroxyl. In certain embodiments, R₁₀ is halogen. In other embodiments, R₁₀ is fluorine. In some embodiments, R₁₀ is C₁₋₆ alkyl. In certain embodiments, R₁₀ is methyl. In certain embodiments, R₁₀ is ethyl In certain embodiments, R₁₀ is propyl. In certain embodiments, R₁₀ is butyl. In certain other embodiments, R₁₀ is —CF₃, —CHF₂, or —CH₂F. In certain embodiments, R₁₀ is hydrogen. In other embodiments, R₁₀ is not hydrogen.

In certain embodiments, R₁₁ is substituted or unsubstituted aliphatic. In some embodiments, R₁₁ is substituted or unsubstituted alkyl. In other embodiments, R₁₁ is —OR_(C). In yet other embodiments, R₁₁ is —N(R_(C))₂. In other embodiments, R₁₁ is —OR_(C). In some embodiments, R₁₁ is —OR_(C) or —CH₂OR_(C), wherein R_(C) is an oxygen protecting group. In certain embodiments, R₁₁ is alkoxy. In certain embodiments, R₁₁ is C₁₋₆ alkoxy. In certain embodiments, R₁₁ is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, R₁₁ is —SR_(C). In some embodiments, R₁₁ is —SR_(C), wherein R_(C) is an sulfur protecting group. In certain embodiments, R₁₁ is alkylthiol. In certain embodiments, R₁₁ is C₁₋₆ alkylthiol. In certain embodiments, R₁₁ is methanethiol. In certain embodiments, R₁₁ is ethanethiol. In certain embodiments, R₁₁ is propanethiol. In certain embodiments, R₁₁ is butanethiol. In certain embodiments, R₁₁ is thiol. In certain embodiments, R₁₁ is hydroxyl, methoxy, or trifluoromethoxy. In certain embodiments, R₁₁ is hydroxyl. In certain embodiments, R₁₁ is halogen. In other embodiments, R₁₁ is fluorine. In some embodiments, R₁₁ is C₁₋₆ alkyl. In certain embodiments, R₁₁ is methyl. In certain embodiments, R₁₁ is ethyl. In certain embodiments, R₁₁ is propyl. In certain embodiments, R₁₁ is butyl. In certain other embodiments, R₁₁ is —CF₃, —CHF₂, or —CH₂F. In certain embodiments, R₁₁ is hydrogen. In other embodiments, R₁₁ is not hydrogen.

In certain embodiments, R_(P) is benzyl. In other embodiments, R_(P) is hydrogen. In yet other embodiments, R_(P) is acyl. In yet other embodiments, R_(P) is a silicon-containing protecting group.

In certain embodiments, a compound of formula VI has one of the following formulae:

An exemplary compound of the formula VI includes:

In other embodiments, the invention provides a compound of formula (V):

wherein R₃, R₄, R₅, R₁₁, and R_(P) are as defined above and described herein.

Exemplary compounds of formula V include:

In certain embodiments, the compound is of formula (IV):

wherein R₃, R₄, R₅, R₁₁, R_(P), R_(Q) and R_(Z) are as defined above and described herein.

Exemplary compounds of formula IV include:

Pharmaceutical Compositions

The present invention also provides a pharmaceutical preparation comprising at least one of the compounds as described above and herein, or a pharmaceutically acceptable derivative thereof, which compounds inhibit the growth of or kill microorganisms, and, in certain embodiments, inhibit the growth of or kill tetracycline-resistant organisms including chlortetracycline-resistant organisms, oxytetracycline-resistant organisms, demeclocycline-resistant organisms, doxycycline-resistant organisms, minocycline-resistant organisms, or any organisms resistant to antibiotics of the tetracycline class used in human or veterinary medicine. In other embodiments, the compounds show cytostatic or cytotoxic activity against neoplastic cells such as cancer cells. In yet other embodiments, the compounds inhibit the growth of or kill rapidly dividing cells such as stimulated inflammatory cells.

As discussed above, the present invention provides novel compounds having antimicrobial and antiproliferative activity, and thus the inventive compounds are useful for the treatment of a variety of medical conditions including infectious diseases, cancer, autoimmune diseases, inflammatory diseases, and diabetic retinopathy. Accordingly, in another aspect of the present invention, pharmaceutical compositions are provided, wherein these compositions comprise any one of the compounds as described herein, and optionally comprise a pharmaceutically acceptable carrier. In certain embodiments, these compositions optionally further comprise one or more additional therapeutic agents, e.g., another antimicrobial agent or another antiproliferative agent. In other embodiments, these compositions further comprise antiinflammatory agent such as aspirin, ibuprofen, acetaminophen, etc., pain reliever, or anti-pyretic.

It will also be appreciated that certain compounds of the present invention can exist in free form for treatment, or where appropriate, as a pharmaceutically acceptable derivative thereof. According to the present invention, a pharmaceutically acceptable derivative includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or any other adduct or derivative which upon administration to a patient in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof, e.g., a prodrug.

As used herein, the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgement, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 66: 1-19, 1977; incorporated herein by reference. The salts can be prepared in situ during the final isolation and purification of the compounds of the invention, or separately by reacting the free base functionality with a suitable organic or inorganic acid. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate, and aryl sulfonate.

Additionally, as used herein, the term “pharmaceutically acceptable ester” refers to esters which hydrolyze in vivo and include those that break down readily in the human body to leave the parent compound or a salt thereof. Suitable ester groups include, for example, those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl moiety advantageously has not more than 6 carbon atoms. Examples of particular esters include formates, acetates, propionates, butyrates, acrylates and ethylsuccinates. In certain embodiments, the esters are cleaved by enzymes such as esterases.

Furthermore, the term “pharmaceutically acceptable prodrugs” as used herein refers to those prodrugs of the compounds of the present invention which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals with undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the invention. The term “prodrug” refers to compounds that are rapidly transformed in vivo to yield the parent compound of the above formula, for example by hydrolysis in blood. A thorough discussion is provided in T. Higuchi and V. Stella, Pro-drugs as Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series, and in Edward B. Roche, ed., Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press, 1987, both of which are incorporated herein by reference.

As described above, the pharmaceutical compositions of the present invention additionally comprise a pharmaceutically acceptable carrier, which, as used herein, includes any and all solvents, diluents, or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. Remington's Pharmaceutical Sciences, Fifteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1975) discloses various carriers used in formulating pharmaceutical compositions and known techniques for the preparation thereof. Except insofar as any conventional carrier medium is incompatible with the anti-cancer compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutical composition, its use is contemplated to be within the scope of this invention. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; Cremophor; Solutol; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil; glycols; such a propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.

Uses of Compounds and Pharmaceutical Compositions

The invention further provides a method of treating infections and inhibiting tumor growth. The method involves the administration of a therapeutically effective amount of the compound or a pharmaceutically acceptable derivative thereof to a subject (including, but not limited to a human or animal) in need of it.

The compounds and pharmaceutical compositions of the present invention may be used in treating or preventing any disease or conditions including infections (e.g., skin infections, GI infection, urinary tract infections, genito-urinary infections, systemic infections), proliferative diseases (e.g., cancer), and autoimmune diseases (e.g., rheumatoid arthritis, lupus). The compounds and pharmaceutical compositions may be administered to animals, preferably mammals (e.g., domesticated animals, cats, dogs, mice, rats), and more preferably humans. Any method of administration may be used to deliver the compound of pharmaceutical compositions to the animal. In certain embodiments, the compound or pharmaceutical composition is administered orally. In other embodiments, the compound or pharmaceutical composition is administered parenterally.

In yet another aspect, according to the methods of treatment of the present invention, bacteria are killed, or their growth is inhibited, by contacting the bacteria with an inventive compound or composition, as described herein. Thus, in still another aspect of the invention, a method for the treatment of infection is provided comprising administering a therapeutically effective amount of an inventive compound, or a pharmaceutical composition comprising an inventive compound to a subject in need thereof, in such amounts and for such time as is necessary to achieve the desired result. In certain embodiments of the present invention, a “therapeutically effective amount” of the inventive compound or pharmaceutical composition is that amount effective for killing or inhibiting the growth of bacteria. The compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for killing or inhibiting the growth of bacteria. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular compound, its mode of administration, its mode of activity, and the like. The compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts.

Furthermore, after formulation with an appropriate pharmaceutically acceptable carrier in a desired dosage, the pharmaceutical compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect. The desired dosage may be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage may be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).

Liquid dosage forms for oral and parenteral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the compounds of the invention are mixed with solubilizing agents such an Cremophor, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and combinations thereof.

Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissues.

Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.

Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, 0 absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.

Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.

Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, ear drops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms can be made by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

It will also be appreciated that the compounds and pharmaceutical compositions of the present invention can be employed in combination therapies, that is, the compounds and pharmaceutical compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another anticancer agent), or they may achieve different effects (e.g., control of any adverse effects).

In still another aspect, the present invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention, and in certain embodiments, includes an additional approved therapeutic agent for use as a combination therapy. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceutical products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

These and other aspects of the present invention will be further appreciated upon consideration of the following Examples, which are intended to illustrate certain particular embodiments of the invention but are not intended to limit its scope, as defined by the claims.

EXAMPLES

General Procedures. All reactions were performed in flame-dried round bottomed or modified Schlenk (Kjeldahl shape) flasks fitted with rubber septa under a positive pressure of argon, unless otherwise noted. Air- and moisture-sensitive liquids and solutions were transferred via syringe or stainless steel cannula. Where necessary (so noted), solutions were deoxygenated by alternative freeze (liquid nitrogen)/evacuation/thaw cycles (≧three iterations). Organic solutions were concentrated by rotary evaporation at ˜25 Torr (house vacuum). Flash column chromatography was performed on silica gel (60 Å, standard grade) as described by Still et al. (Still, W. C.; Kahn, M.; Mitra, A. J. Org. Chem. 1978, 43, 2923-2925; incorporated herein by reference). Analytical thin-layer chromatography was performed using glass plates pre-coated with 0.25 mm 230-400 mesh silica gel impregnated with a fluorescent indicator (254 nm). Thin layer chromatography plates were visualized by exposure to ultraviolet light and/or exposure to eerie ammonium molybdate or an acidic solution of p-anisaldehyde followed by heating on a hot plate.

Materials. Commercial reagents and solvents were used as received with the following exceptions. Chlorotrimethylsilane, triethylamine, diisopropylamine, 2,2,6,6-tetramethylpiperidine, N,N,N′,N′-tetramethylethylenediamine, DMPU, HMPA, and N,N-diisopropylethylamine were distilled from calcium hydride under dinitrogen atmosphere. Benzene, dichloromethane, ethyl ether, methanol, pyridine, tetrahydrofuran, hexane, acetonitrile, N,N-dimethylformamide, and toluene were purified by the method of Pangborn et al. (Pangborn, A. B.; Giardello, M. A.; Grubbs, R. H.; Rosen, R. K.; Timmers, F. J. Organometallics 1996, 15, 1518-1520; incorporated herein by reference). The molarity of n-butyllithium, s-butyllithium, and t-butyllithium were determined by titration with a tetrahydrofuran solution of 2-butanol using triphenylmethane as an indicator (Duhamel, L.; Palquevent, J.-C. J. Org. Chem. 1979, 44, 3404-3405; incorporated herein by reference).

Instrumentation. Proton nuclear magnetic resonance (¹H NMR) spectra and carbon nuclear magnetic resonance (¹³C NMR) were recorded with Varian Unity/Inova 600 (600 MHz), Varian Unity/Inova 500 (500 MHz/125 MHz), or Varian Mercury 400 (400 MHz/100 MHz) NMR spectrometers. Chemical shifts for protons are reported in parts per million scale (δ scale) downfield from tetramethylsilane and are referenced to residual protium in the NMR solvents (CHCl₃: δ 7.26, C₆D₅H: δ 7.15, D₂HCOD: δ 3.31, CDHCl₂: δ 5.32, (CD₂H)CD₃SO: δ 2.49). Chemical shifts for carbon are reported in parts per million (δ scale) downfield from tetramethylsilane and are referenced to the carbon resonances of the solvent (CDCl₃: δ 77.0, C₆D₆: δ 128.0, D₃COD: δ 44.9, CD₂Cl₂: δ 53.8, (CD₃)₂SO: δ 39.5). Data are represented as follows: chemical shift, multiplicity (s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet, br=broad), integration, coupling constant in Hz, and assignment. Infrared (IR) spectra were obtained using a Perkin-Elmer 1600 FT-IR spectrophotometer referenced to a polystyrene standard. Data are represented as follows: frequency of the absorption (cm⁻¹), intensity of absorption (s=strong, sb=strong broad, m=medium, w=weak, br=broad), and assignment (where appropriate). Optical rotations were determined on a JASCO DIP-370 digital polarimeter equipped with a sodium lamp source using a 200-μL or 2-mL solution cell. High resolution mass spectra were obtained at the Harvard University Mass Spectrometry Facilities.

Example 1 Preparation of Enone 4

Step 1. Synthesis of Meso-Diol 2.

A 3-L, two-necked, round-bottomed flask equipped with a Teflon-coated magnetic stirring bar and a thermometer was charged with enedione 1 (50 g, 287 mmol, 0.1 equiv) and methanol (960 mL). Enedione 1 was prepared in >100 g batches according to the procedure in Oda, et al., Organic Syntheses (1996) 73: 253-261. The reaction mixture was stirred at 23° C. until enedione 1 completely dissolved, whereupon cerium trichloride heptahydrate (214 g, 574 mmol, 2 equiv) was added and the resulting slurry was stirred for 1 h at 23° C. (resulting in an orange homogeneous reaction mixture). The reaction flask was placed in an ice-water bath until an internal temperature of 5° C. was reached. Sodium borohydride (13.6 g, 359 mmol, 1.23 equiv) was added to the cold reaction solution at a rate such that the internal temperature remained below 8° C. (addition over ˜1.5 h, CAUTION—EVOLUTION OF HYDROGEN GAS). The resulting slurry was stirred for 30 min at 5-8° C., then saturated aqueous ammonium chloride solution (1 L) was added over the course of 30 min. The reaction flask was removed from the cooling bath and allowed to warm to 23° C. The homogeneous product mixture was partitioned between half-saturated aqueous ammonium chloride solution (1 L) and ethyl acetate (1 L). The layers were separated. The aqueous layer was extracted with two 1-L portions of ethyl acetate. The organic layers were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide meso-diol 2 (49.5 g, 97%) as an off-white solid that was used directly in the next step. Meso-diol 2 is a known compound; see, for example, Wilson, et al., J. Chem. Soc., Chem. Commun. (1970) 213-214 and Marchand, et al., J. Org. Chem. (1986) 51: 1622-1625.

Step 2. Synthesis of Alcohol 3.

A 2-L, one-necked, round-bottomed flask equipped with a Teflon-coated magnetic stirring bar was charged with meso-diol 2 (47 g, 264 mmol, 1 equiv), immobilized lipase PS from Amano (47 g), isopropenyl acetate (87.2 mL, 792 mmol, 3 equiv) and triethylamine (754 mL). The resulting slurry was stirred for 22 h at 23° C., then filtered through a 350-mL sintered glass funnel of medium porosity. The filter cake was rinsed with ethyl acetate (800 mL), then the filtrate was concentrated. The yellow concentrate was dissolved with ethyl acetate (800 mL), then was washed sequentially with 0.2 N aqueous hydrochloric acid solution (500 mL), water (500 mL), and saturated aqueous sodium chloride solution (500 mL). The washed organic solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide alcohol 3 (55.4 g, 95%) as a yellow oil that was used directly in the next step. Alcohol 3 is a known compound; see, for example, Takano, et al., Synthesis 1993, 948-950; Nakashima, et al., Synlett 1999, 1405-1406; and Konno, et al., A Practical Preparation of Versatile Cyclohexenoid Chiral Building Blocks. Synthesis 1999, 1135-1140.

Step 3. Synthesis of Enone 4.

A 3-L, three-necked, round-bottomed flask was equipped with a Teflon-coated magnetic stirring bar, a thermometer, a reflux condenser, and a glass stopcock. The reaction flask was flushed with argon, then was charged with a solution of alcohol 3 (55.4 g, 252 mmol, 1 equiv) in acetonitrile (840 mL). To the stirring solution was added sequentially ammonium formate (19.9 g, 315 mmol, 1.25 equiv) and dichlorobis(triphenylphosphine)palladium(II) (1.8 g, 2.52 mmol, 0.01 equiv) (resulting in a yellow slurry). The reaction solution was heated to reflux (internal temperature of 100-105° C.) and stirring was continued for 20 min. The resulting dark-orange, near-homogeneous solution was removed from the hot oil bath and allowed to cool to 23° C. The product mixture was transferred to a 3-L, one-necked, round-bottomed flask with a minimal amount of ethyl acetate and the resulting organic solution was concentrated. The dark-red concentrate was suspended in ethyl acetate (500 mL), then was filtered through a pad of Celite rinsing with ethyl acetate (500 mL). The combined organics were washed sequentially with half-saturated aqueous sodium bicarbonate solution (1 L) and half-saturated aqueous sodium chloride solution (1 L). The washed organic solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash column chromatography (7:1 hexanes-ethyl acetate grading to 4:1 hexanes-ethyl acetate) to provide enone 4 (31.9 g, 79%) as a yellow oil which solidified at −20° C. The enantiomeric excess of the purified product was determined to be >99% by chiral GC analysis (Restek Rt-βDexsm column, 30 m, 0.25 mmID, oven T=40° C. for 5 min then increase 2° C./min, t_(R)(major, enone enantiomer 4)=55.202 min, t_(R)(minor, enone enantiomer 4)=56.453 min. Enone 4 is a known compound; see, for example, Takano, et al., Synthesis (1993) 948-950.

Example 2 Preparation of Isoxazole 7

Step 1. Synthesis of Carboxylic Acid 6.

A 5-L, three-necked, oven dried round-bottomed flask equipped with a mechanical stirrer, a 500-mL pressure-equalizing addition funnel, and a thermometer was flushed with argon. The flask was charged with a solution of isoxazole 5 (155 g, 668 mmol, 1 equiv) in THF (3 L). Isoxazole 5 is a known compound; see, for example, Charest, et al. A Convergent Enantioselective Route to Structurally Diverse 6-Deoxytetracycline Antibiotics. Science 2005, 308, 395-398 and Myers, et al. Synthesis of Tetracyclines and Analogues Thereof US 2005/0282787, published Dec. 22, 2005. The reaction flask was placed in a dry ice-acetone bath and the solution allowed to cool to −78° C., whereupon a solution of n-butyllithium in hexanes (2.5 M, 280 mL, 701 mmol, 1.05 equiv) was added dropwise through the addition funnel at a rate such that the internal reaction temperature was <−68° C. (addition time ˜40 min). The resulting slurry was stirred for 1 h at −78° C., whereupon carbon dioxide was bubbled into the reaction mixture through a dry 8-gauge stainless-steel needle for 2 h at which point the reaction solution became near homogeneous. The reaction flask was removed from the cooling bath and placed into a 23° C. water bath and the reaction mixture was allowed to warm to 23° C. Argon was bubbled through the 23° C. reaction mixture for 15 min, then 1 N aqueous sodium hydroxide solution (1.4 L) and hexanes (200 mL) was added. The resulting biphasic mixture was stirred for 25 min, then was transferred to a 6-L separation funnel. Hexanes (800 mL) and ethyl acetate (200 mL) was added and the biphasic mixture was shaken vigorously, then the layers were separated. The organic layer was extracted with two 200-mL portions of 0.5 N aqueous sodium hydroxide solution. The combined aqueous layers were washed with hexanes-ethyl acetate (2:1, 500 mL). The aqueous alkali layer was transferred to a 3-L round-bottomed flask equipped with a Teflon-coated magnetic stirring bar, then the flask was placed into a 23° C. water bath. The stirring aqueous solution was made acidic with 12 N hydrochloric acid (pH ˜6-6.5 by litmus paper test, CAUTION—GAS EVOLUTION). The acidic aqueous solution was stirred for 15 minutes at 23° C., then sodium chloride (475 g) was added. The aqueous solution was transferred to a 6-L separation funnel, then extracted with one 4-L portion of dichloromethane and four 700-mL portions of dichloromethane. The combined organic layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide carboxylic acid 6 (146 g) as a pale yellow solid that was used directly in the next step.

Step 2. Synthesis of Methyl Ester 7.

A 5-L, three-necked, oven dried round-bottomed flask equipped with a mechanical stirrer, a 500-mL pressure-equalizing addition funnel, and a thermometer was flushed with argon. The reaction flask was charged with a solution of the carboxylic acid 6 (146 g, 668 mmol, 1 equiv) in dichloromethane (3.5 L) and N,N-dimethylformamide (1.98 mL, 26.3 mmol, 0.05 equiv). The resulting white slurry was cooled to ˜8° C., then a solution of oxalyl chloride in dichloromethane (2 M, 342 mL, 685 mmol, 1.3 equiv) was added dropwise through the funnel over the course of 2 h. The flask was removed from the cooling bath, then the reaction mixture was stirred for 3 h at 23° C. The reaction flask was placed into an ice-water bath and the reaction mixture was allowed to cool to 5° C. A separate 5-L, two-necked, oven dried round-bottomed flask equipped with a Teflon-coated magnetic stirring bar was charged with 4-dimethylaminopyridine (1.92 g, 15.8 mmol, 0.03 equiv), dichloromethane (400 mL), methanol (107 mL, 2.63 mol, 5 equiv) and triethylamine (221 mL, 1.58 mol, 3 equiv), then the resulting solution was cooled to 0° C. To this cold solution was added dropwise by cannula the above cold carboxylic acid chloride solution. The resulting homogeneous brown solution was removed from the cooling bath and stirred for 3 h at 23° C., then saturated aqueous sodium bicarbonate solution (1 L) was added. The resulting biphasic mixture was stirred for 20 min, then transferred to a separation funnel and the layers separated. The organic layer was washed sequentially with two 800-mL portions of water and one 800-mL portion of saturated aqueous sodium chloride solution. The washed organic solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The concentrate was dissolved in dichloromethane-ethyl acetate (1:1, 400 mL), then hexanes (800 mL) was added. The product mixture was shaken by hand for 2 min, then filtered through silica gel rinsing with hexanes-acetone (1:1, 1.5 L). The filtrate was concentrated by high vacuum for 4 h at 50° C. to provide the methyl ester 7 (134 g, 87%). The methyl ester 7 is a known compound; see Stork, et al. Stereocontrolled Synthesis of (±)-12a-Deoxytetracycline. J. Am. Chem. Soc. 1996, 118, 5304-5305. TLC (50% acetone-hexanes): R_(f)=0.55 (UV, CAM). ¹H NMR (600 MHz, CDCl₃), δ: 7.49-7.48 (m, 2H), 7.41-7.34 (m, 3H), 5.36 (s, 2H), 3.90 (s, 2H), 3.85 (s, 3H), 2.36 (s, 6H). ¹³C NMR (125 MHz, CDCl₃), δ: 176.2, 168.9, 161.5, 135.6, 128.5, 128.3, 127.8, 102.1, 71.7, 53.6, 51.8, 45.2.

Example 3 Synthesis of Michael-Claisen Product 9

A solution of sodium bis(trimethylsilyl)amide in tetrahydrofuran (1 M, 27.6 mL, 27.6 mmol, 1.2 equiv) was added dropwise to a solution of methyl ester 7 (8.02 g, 27.5 mmol, 1.2 equiv) in tetrahydrofuran (137 mL) at −78° C. over the course of seven min resulting in a dark brown solution. The reaction flask was placed in a −20° C. cooling bath and the solution was stirred for 30 min at this temperature. The resulting dark brown slurry was cooled to −78° C., then a solution of enone 4 (3.67 g, 22.9 mmol, 1 equiv) in tetrahydrofuran (22 mL) was added dropwise over the course of four min. The reaction mixture was stirred for 40 minutes was at −60° C. then cooled to −78° C., whereupon a solution of potassium bis(trimethylsilyl)amide in toluene (0.5 M, 48 mL, 24 mmol, 1.05 equiv) was added dropwise over the course of 20 minutes. The resulting reaction mixture was warmed to −20° C. over 40 min and stirring continued at this temperature for 6 h, then saturated aqueous ammonium chloride solution (80 mL) was added. The reaction flask was removed from the cooling bath and the biphasic product solution was allowed to warm to 23° C., then saturated aqueous sodium chloride solution (50 mL) and ethyl acetate (200 mL) was added and stirring was continued for 10 min. The phases were separated and the aqueous phase was extracted with two 100-mL portions of ethyl acetate. The organic layers were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes, grading to 20% ethyl acetate-hexanes) to provide the Michael-Claisen product 9 as a pale yellow solid (7.4 g, 77%). TLC (33% ethyl acetate-hexanes): R_(f)=0.38 (UV, CAM). [α]²³ _(D) −7.28 (c 0.70, CHCl₃). ¹H NMR (600 MHz, CDCl₃), δ: 15.16 (s, 1H), 7.50-7.49 (m, 2H), 7.38-7.32 (m, 3H), 6.04-6.00 (m, 2H), 5.39-5.34 (m, 2H), 3.61 (d, J=6.5 Hz, 1H), 3.20 (s, 1H), 2.91 (s, 1H), 2.87 (dd, 1H, J=4.0, 9.0 Hz), 2.75-2.71 (m, 2H), 2.17-2.10 (m, 1H), 2.13 (s, 6H), 1.80 (dd, 1H, J=5.0, 15.0 Hz), 1.46 (d, 1H, J=8.5 Hz), 1.42 (d, 1H, J=8.5 Hz). ¹³C NMR (125 MHz, CDCl₃), δ: 183.8, 180.9, 176.6, 167.6, 135.6, 135.4, 135.1, 128.4, 128.3, 128.2, 107.9, 105.4, 72.2, 58.2, 50.9, 49.5, 46.8, 42.7, 41.9, 37.5, 34.1, 26.0. IR (neat), cm⁻¹: 2964 (s), 2937 (s), 1627 (s), 1610 (s), 1573 (s), 1506 (s), 1330 (s). HRMS (ESI): Calcd for (C₂₅H₂₆N₂O₄+Na)⁺: 441.1785. Found: 441.1793.

Example 4 Synthesis of Retro-Diels-Alder Product 10

A special setup was constructed for this transformation (see FIG. 1). A 1-L, 3-necked, round-bottomed flask was charged with 9 (4.9 g, 11.7 mmol, 1 equiv), diphenyl ether (490 mL) and dimethyl maleate (7.3 mL, 58.3 mmol, 5 equiv). The homogeneous solution was degassed by bubbling with argon for 30 min. The degassed solution was passed through a stainless steel loop (304 ss, ⅛ in ×0.147 in ×10 ft, VWR) preheated to 250° C. then a 23° C. water cooling bath using a liquid pump (FMI Q pump, CERAMPUMP®) at a rate of ˜14 mL per min into a 1-L round-bottomed flask. The flask containing the product mixture was placed into a 20° C. water bath and hexanes (400 mL) was added, then a solution of hydrogen chloride in ether (2.0 N, 9.9 mL, 19.8 mmol, 1.7 equiv) was added dropwise. The resulting mixture was rigorously stirred for 45 min during which time a solid formed. The slurry was filtered. The filter cake was washed with three 30-mL portions of hexanes and the washed filter cake was air-dried for 1 h. The dried filter cake was dissolved with aqueous dipotassium hydrogenphosphate solution (1 N, 60 mL) and ethyl acetate (150 mL). The resulting biphasic mixture was stirred for 30 min at 23° C. The layers were separated. The aqueous layer was extracted with ethyl acetate (100 mL). The organic phases were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue obtained was purified by flash-column chromatography on silica gel (10% ethyl acetate-hexanes grading to 20% ethyl acetate-hexanes) to provide the retro-Diels-Alder product 10 (2.67 g, 65%) as a pale yellow solid. TLC (33% ethyl acetate-hexanes): R_(f)=0.24 (UV, CAM). [α]²³ _(D) 373 (c 0.65, CHCl₃). ¹H NMR (600 MHz, CDCl₃), δ: 15.06 (s, 1H), 7.52-7.51 (m, 2H), 7.40-7.33 (m, 3H), 6.60 (ddd, 1H, J=2.4, 6.0, 9.0 Hz), 6.04 (dd, 1H, J=3.0, 9.0 Hz), 5.40 (s, 2H), 3.84 (d, 1H, J=7.2 Hz), 3.40 (dt, 1H, J=7.2, 15.6 Hz), 2.96-2.89 (m, 1H), 2.37-2.32 (m, 1H), 2.27 (s, 6H). ¹³C NMR (125 MHz, CDCl₃), δ: 181.2, 175.6, 172.6, 167.6, 142.3, 135.2, 128.5, 128.4, 128.3, 124.2, 107.7, 102.1, 73.3, 57.6, 41.9, 34.9, 25.6. IR (neat), cm⁻¹: 2978 (s), 2939 (s), 2831 (s), 2360 (s), 1627(s), 1566 (s), 1504 (s). HRMS (ESI): Calcd for (C₂₀H₂₀N₂O₄+H)⁺: 353.1496. Found: 353.1508.

Example 5 Synthesis of Alcohol 11

A 100-mL, single-necked, round-bottomed flask was equipped with a Teflon-coated magnetic stirring bar and charged with lithium chloride (189 mg, 4.52 mmol, 1.1 equiv). The flask was flame dried under vacuum with stirring. The flask was flushed with argon three times, then allowed to cool to 23° C. under argon. The flask was charged with a solution of 10 (1.45 g, 4.11 mmol, 1 equiv) in 1,2-dimethoxyethane (12 mL). The resulting slurry was cooled to −30° C., then a solution of lithium bis(trimethylsilyl)amide in 1,2-dimethoxyethane [prepared by adding a solution of n-butyllithium in hexanes (2.5 M, 1.81 mL, 4.52 mmol, 1.1 equiv) dropwise to a solution of hexamethyldisilazane (0.988 mL, 4.73 mmol, 1.15 equiv) in anhydrous 1,2-dimethoxyethane (8 mL) at −78° C., followed by stirring at 0° C. for 30 min] was added dropwise over the course of 3 min. The resulting yellow slurry was stirred for 10 min at −30° C., then a solution of trans-2-(phenylsulfonyl)-3-phenyloxaziridine (1.37 g, 4.93 mmol, 1.2 equiv) (Vishwakarma, et al., (±)-trans-2-(phenylsulfonyl)-3-Phenyloxaziridine. Organic Syntheses 1988, 66, 203-207) in 1,2-dimethoxyethane (6 mL) was added to the reaction mixture dropwise by syringe over the course of 5 min. The transfer was quantitated with additional 1,2-dimethoxyethane (2 mL). The resulting reaction mixture was stirred for 15 h at −30° C. during which time a dark blue solution formed, then 1 N aqueous hydrochloric acid solution (20 mL) and water (20 mL) was added. The reaction flask was removed from the cooling bath and the biphasic product mixture was and allowed to warm to 23° C., then poured into a separation funnel. The layers were separated. The organic layer was extracted with a 0.5 N aqueous hydrochloric acid solution (4 mL). The combined acid aqueous layers were washed with two 20-mL portions of hexane-ethyl acetate (2:1). These new organic layers were combined and the combined solution was extracted with water (20 mL). The water layer was combined with the aqueous acid layers and the combined solution was neutralized with potassium phosphate dibasic (7.65 g). Dichloromethane (100 mL) was added and the resulting biphasic mixture was stirred for 15 min. The layers were separated. The aqueous layer was extracted with two 30-mL portions of dichloromethane. The organic layers were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide alcohol 11 (1.46 g) as a purple solid that was used directly in the next step. An analytical sample was prepared by radial chromatography (1:1 hexanes-ethyl acetate grading to 1:1 hexanes-acetone). White foam. TLC (50% acetone-hexanes): R_(f) 0.42 (UV, CAM). [α]²³ _(D) 373 (c 0.65, CHCl₃). ¹H NMR (500 MHz, CDCl₃), δ: 7.49-7.47 (m, 2H), 7.40-7.34 (m, 3H), 7.00-6.97 (m, 1H), 6.24 (dd, 1H, J=2.5, 10.5 Hz), 5.36 (s, 2H), 4.65 (br s, 1H), 4.48 (d, 1H, J=5.0 Hz), 3.10 (dt, 1H, J=5.0, 10.5 Hz), 2.80 (dt, 1H, J=5.5, 20.0 Hz), 2.62 (s, 6H), 2.49-2.41 (m, 1H). ¹³C NMR (125 MHz, CDCl₃), δ: 195.0, 185.7, 180.4, 167.9, 149.8, 134.9, 128.6, 128.5, 128.2, 126.9, 106.1, 80.4, 72.4, 59.9, 47.1, 44.5, 26.5. [α]²³ _(D) −183 (c 0.55, CHCl₃). IR (neat), cm⁻¹: 3435 (s), 2926 (m), 1703 (s), 1683 (s), 1595(s), 1473 (s), 1369 (s). HRMS (ESI): Calcd for (C₂₀H₂₀N₂O₅+H)⁺: 391.1264. Found: 391.1266.

Example 6 Synthesis of Enone Intermediate 12A

Epimerization. A 100-mL, single-necked, round-bottomed flask equipped with a Teflon-coated magnetic stirring bar was flushed with argon. The flask was charged with a solution of alcohol 11 (1.46 g, 3.96 mmol, 1 equiv) in tetrahydrofuran (10 mL), methanol (10 mL), and a 2 M aqueous sodium dihydrogen phosphate solution (6 mL). The resulting biphasic mixture was degassed by bubbling with argon for 30 min. The mixture was stirred at 52° C. for 15 h. The flask was removed from the heating bath and the product mixture allowed to cool to 23° C., then water (15 mL), dipotassium hydrogenphosphate (7.83 g), and dichloromethane (40 mL) was added and the resulting biphasic mixture was stirred for 10 min. The layers were separated. The aqueous layer was extracted with two 40-mL portions of dichloromethane. The organic layers were combined and the combined layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide a purple residue that was used directly in the next step.

Silylation. A 100-mL, single-necked, round-bottomed flask equipped with a Teflon-coated magnetic stirring bar was flame-dried, then allowed to cool to 23° C. under argon. The flask was charged with a solution of the product obtained above in dichloromethane (20 mL). The solution was cooled to 0° C., whereupon 2,6-Lutidine (0.813 mL, 7.14 mmol, 1.8 equiv) and tert-butyldimethylsilyl trifluoromethanesulfonate (1.28 mL, 5.56 mmol, 1.4 equiv) were added sequentially dropwise by syringe. The reaction mixture was stirred for 15 min at 0° C., then the cooling bath was removed. The reaction solution was stirred for 20 min at 23° C., then was partitioned between aqueous potassium phosphate buffer solution (pH 7, 0.05 M, 40 mL) and dichloromethane (35 mL). The layers were separated. The aqueous layer was extracted with one 40-mL portion of dichloromethane. The organic layers were combined and the combined layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (100% dichloromethane, grading to 2% ethyl acetate-dichloromethane) to provide the enone 12A (990 mg, 50% yield over 3 steps) as a light-yellow foam. TLC (20% ethyl acetate-hexanes): R_(f)=0.34 (UV, CAM). ¹H NMR (600 MHz, CDCl₃), δ: 7.51 (d, 2H, J=1.5 Hz, ArH), 7.50-7.34 (m, 3H, ArH), 6.94 (m, 1H, ═CHCH₂), 6.10 (ddd, 1H, J=10.3, 1.5, 1.5 Hz, ═CHC(O)), 5.36 (m, 2H, OCH₂Ph), 3.79 (d, 1H, J=10.7 Hz, CHN(CH₃)₂), 2.83 (m, 2H, ═CHCH₂), 2.78 (m, 1H, CHCHN(CH₃)₂), 2.46 (s, 6H, N(CH₃)₂), 0.84 (s, 9H, SiC(CH₃)₃), 0.27 (s, 3H, SiCH₃), 0.06 (s, 3H, SiCH₃).

Synthesis of C12a-methoxy AB enone 12B

A solution of alcohol 11 (70 mg, 0.190 mmol, 1 equiv) in tetrahydrofuran (2 mL) at 23° C. was added dropwise by cannula to a stirring solution of lithium bis(trimethylsilyl)amide (1 M in THF, 230 μL, 0.228 mmol, 1.2 equiv) and hexamethylphosphoramide (66 μL, 0.380 mmol, 2 equiv) in tetrahydrofuran (2 mL) at −78° C. The resulting solution was stirred for 5 min at −78° C. whereupon methyl trifluoromethanesulfonate (43 μL, 0.380 mmol, 2 equiv) was added. The mixture was stirred at −78° C. for 30 min then the cooling bath was removed and stirring continued for 5 min with warming, whereupon water (2 mL) was added. The biphasic product mixture was poured into a separation funnel containing saturated aqueous ammonium chloride solution (10 mL) and ethyl acetate (10 mL). The layers were separated. The aqueous layer was extracted with ethyl acetate (10 mL). The organic layers were combined and the combined solution dried over sodium sulfate. The dried solution was filtered and the filtrate concentrated. The residue was purified by flash-column chromatography on silica gel (100% dichloromethane initially, grading to 8% ethyl acetate-dichloromethane) to provide the product 12B as a light yellow foam (53 mg, 73%). ¹H NMR (600 MHz, CDCl₃) δ: 7.50-7.48 (m, 2H), 7.40-7.34 (m, 3H), 7.02-6.99 (m, 1H), 6.11 (m, 1H), 5.33 (AB q, 2H), 3.82 (d, 1H, J=10.5 Hz), 3.60 (s, 3H), 2.91-2.80 (m, 3H), 2.46 (s, 6H).

Example 7 Synthesis of Phenyl Ester 13

A solution of n-butyllithium in hexanes (2.5 M, 6.9 mL, 17.2 mmol, 1 equiv) was added dropwise by syringe to a stirring solution of isoxazole 5 (4 g, 17.2 mmol, 1 equiv) in tetrahydrofuran (170 mL) at −78° C. The resulting red slurry was stirred for 45 min at −78° C., then added dropwise by cannula to a stirring solution of phenyl chloroformate (2.3 mL, 18.1 mmol, 1.05 equiv) in tetrahydrofuran (50 mL) at −78° C. over the course of 20 min. The resulting yellow slurry was stirred for 2.5 h at −78° C., then the flask was removed from the cooling bath and reaction mixture allowed to warm to 23° C. Saturated aqueous ammonium chloride solution (500 mL) and ethyl acetate (200 mL) was added, then the resulting biphasic mixture poured into a separation funnel. The layers were separated. The aqueous layer was extracted with two 200-mL portions of ethyl acetate. The organic layers were combined and the combined layers were dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (25% ethyl acetate-hexanes grading to 50% ethyl acetate-hexanes) to provide the phenyl ester 13 (3.6 g, 59%) as a yellow oil which slowly solidified. TLC (50% Et₂O-hexanes): R_(f)=0.17 (UV, KMnO₄). ¹H NMR (600 MHz, CDCl₃), δ: 7.50-7.48 (m, 2H), 7.43-7.25 (m, 6H), 7.19-7.17 (m, 2H), 5.41 (s, 2H), 3.98 (s, 2H), 2.39 (s, ¹³C NMR (125 MHz, CDCl₃), δ: 177.2, 169.0, 159.5, 150.1, 135.5, 129.5, 128.5, 128.3, 127.6, 126.1, 121.6, 101.8, 71.8, 53.8, 45.3. IR (neat), cm⁻¹: 2943 (m), 2785 (m), 1707 (s), 1508 (s). HRMS (ESI): Calcd for (C₂₀H₂₀N₂O₄+H)⁺: 353.1496. Found: 353.1501.

Example 8 Synthesis of Enone 14

Conjugate addition. An oven-dried 200-mL, single-necked, round-bottomed flask equipped with a magnetic stirring bar was charged with copper iodide (3 g, 15.6 mmol, 2.5 equiv) and tetrahydrofuran (60 mL). The resulting slurry was cooled to 0° C., whereupon a solution of methyllithium in diethoxymethane (3 M, 10.3 mL, 30.9 mmol, 4.95 equiv) was added dropwise by syringe. The resulting orange slurry was stirred for 20 min at 0° C. resulting in a light-brown, homogeneous reaction mixture, then cooled to −78° C. resulting in a heterogeneous solution. A separate dry round-bottomed flask was charged with enone 4 (1 g, 6.24 mmol, 1 equiv), hexamethylphosphoramide (3.3 mL, 18.7 mmol, 3 equiv), trimethylsilylchloride (2.4 mL, 18.7 mmol, 3 equiv), and tetrahydrofuran (30 mL). This solution was added dropwise by cannula to the above −78° C. organo-copper solution. Additional tetrahydrofuran (5 mL) was used to quantitate the transfer. The resulting homogeneous solution was stirred for 20 min at −78° C., then diluted with ethyl acetate-hexanes (1:1, 60 mL). The reaction flask was removed from the cooling bath, then saturated aqueous ammonium chloride solution-14.8 N aqueous ammonium hydroxide solution (15:1, pH˜9.5, 60 mL) was added. The resulting slurry was stirred for 5 min at 23° C., then partitioned between saturated aqueous ammonium chloride solution-14.8 N aqueous ammonium hydroxide solution (15:1, pH˜9.5, 250 mL) and ethyl acetate-hexanes (60 mL). The layers were separated. The organic layer was washed with two 50-mL portions of saturated aqueous ammonium chloride solution and one portion 50-mL portion of saturated aqueous sodium chloride solution. The washed organic solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide the intermediate (trimethylsilyl)enol ether contaminated with hexamethylphosphoramide that was used directly in the next step.

Enone formation. The above product (trimethylsilyl)enol ether was dissolved in dimethyl sulfoxide (50 mL). Palladium diacetate (1.5 g, 6.55 mmol, 1.05 equiv) was added in one portion and the resulting black slurry stirred for 20 h at 23° C., then filtered through a pad of silica gel rinsing with ethyl acetate (100 mL). The filtrate was partitioned between hexanes (100 mL) and water (200 mL). The layers were separated. The organic layer was washed with two 100-mL portions of water and one 100-mL portion of saturated aqueous sodium chloride solution. The washed organic solution was dried over sodium sulfate. The dried solution of filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (30% ethyl acetate-hexanes) to provide enone 14 (808 mg, 74% over 2 steps) as a yellow oil which solidifies at −20° C. TLC (25% ethyl acetate-hexanes): R_(f)=0.24 (UV, KMnO₄). ¹H NMR (600 MHz, CDCl₃), δ: 6.10-6.06 (m, 2H), 5.74-5.73 (m, 1H), 3.36 (d, 1H, J=1.2 Hz), 3.01 (s, 1H), 2.81 (dd, 1H, J=4.0, 10.1 Hz), 2.77-2.73 (m, 1H), 2.49 (dd, 1H, J=10.4, 20 Hz), 1.92 (d, 1H, J=20 Hz), 1.82 (s, 3H), 1.42-1.40 (m, 1H), 1.35-1.33 (m, 1H). ¹³C NMR (125 MHz, CDCl₃), δ: 200.8, 160.8, 137.8, 134.1, 126.4, 49.1, 48.5, 48.3, 47.7, 34.3, 32.4, 24.4. IR (neat), cm⁻¹: 2965, 2936, 1651 (s). HRMS (ESI): Calcd for (C₁₂H₁₄O+Na)⁺: 197.0937. Found: 197.0962.

Example 9 Synthesis of Michael-Claisen Product 15

A solution of lithium bis(trimethylsilyl)amide in tetrahydrofuran (1 M, 1.15 mL, 1.15 mmol, 2 equiv) was added dropwise by syringe to a stirring solution of phenyl ester 13 (405 mg, 1.15 mmol, 2 equiv) in tetrahydrofuran (12 mL) at −78° C. The resulting brown heterogeneous mixture was stirred for 30 min at −20° C. and then cooled to −78° C., whereupon a solution of enone 14 (100 mg, 0.574 mmol, 1 equiv) in tetrahydrofuran (5 mL) was added dropwise by syringe. Additional tetrahydrofuran (1 mL) was used to quantitate the transfer. The resulting slurry was stirred for 5 min at −78° C., then the flask was removed from the cooling bath and the reaction mixture was allowed to warm to 23° C. and stirring was continued for 24 h during which time the reaction became homogeneous. Water (1 mL) was added and the resulting biphasic mixture was concentrated. Ethyl acetate (15 mL) was added to the residue and the resulting organic solution was washed with two 10-mL portions of a 1 N aqueous sodium hydroxide solution. The washed organic solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash-column chromatography on silica gel (10% acetone-hexanes) to provide the Michael-Claisen product 15 (116 mg, 47%) as an oil which slowly solidified. TLC (10% acetone-hexanes): R_(f)=0.20 (UV, KMnO₄). ¹H NMR (600 MHz, CDCl₃), δ: 14.55 (s, 1H), 7.51-7.52 (m, 2H), 7.40-7.33 (m, 3H), 6.20 (dd, 1H, J=3.2, 5.5 Hz), 6.12 (dd, 1H, J=3.2, 5.7 Hz), 5.40-5.35 (m, 2H), 3.35 (s, 1H), 3.22 (s, 1H), 2.93-2.91 (m, 2H), 2.85-2.81 (m, 1H), 2.79-2.74 (m, 2H), 2.18 (s, 6H), 1.56-1.54 (m, 1H), 1.43 (d, 1H, J=8.2 Hz), 1.28 (d, 1H, J=3.4 Hz), 1.07 (s, 3H). ¹³C NMR (125 MHz, CDCl₃), δ: 184.4, 178.5, 177.1, 167.9, 137.4, 135.2, 135.2, 128.6, 128.5, 128.3, 110.5, 107.1, 72.3, 66.5, 51.1, 48.6, 47.1, 42.5, 42.1, 39.0, 36.3, 33.8, 31.9. IR (neat), cm⁻¹: 2961, 2926, 1630 (s), 1611, 1574, 1506 (s), 1476, 1454. HRMS (ESI): Calcd for (C₂₆H₂₈N₂O₄+H)⁺: 433.2122. Found: 433.2110.

Example 10 Synthesis of Michael Addition Product 17

A solution of n-butyllithium in hexanes (2.5 M, 2.91 mL, 7.27 mmol, 1.15 equiv) was added to a solution of 1,3-dithiane (862 mg, 6.95 mmol, 1.1 equiv) in tetrahydrofuran (60 mL) at −78° C. The resulting solution was stirred at this temperature for 30 min, at which point hexamethylphosphoramide (2.44 mL, 13.9 mmol, 2.2 equiv) was added. After stirring at −78° C. for a further 2 min, a solution of the AB enone 16 (3.05 g, 6.32 mmol, 1 equiv) in tetrahydrofuran (25 mL) was added dropwise via syringe to the reaction solution. The brownish-yellow reaction mixture was stirred at −78° C. for 40 min whereupon trimethylsilyl chloride (1.20 mL, 9.48 mmol, 1.5 equiv) was added. After stirring at −78° C. for 40 min, aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 100 mL) was added to the reaction solution. The resulting mixture was allowed to warm to 23° C., then was extracted with dichloromethane (3×100 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by flash-column chromatography (8% ethyl acetate-hexanes), affording the Michael addition product 17 as a foamy white solid (3.85 g, 90%). R_(f)=0.53 (30% ethyl acetate-hexanes); NMR (500 MHz, CDCl₃) δ 7.48 (d, 2H, J=7.0 Hz), 7.38-7.31 (m, 3H), 5.36 (AB quartet, 2H, J=12.0 Hz, Δν=34.0 Hz), 4.98 (d, 1H, J=3.0 Hz), 4.12 (d, 1H, J=5.0 Hz), 3.89 (d, 1H, J=9.5 Hz), 2.96-2.82 (m, 5H), 2.46 (s, 6H), 2.34-2.29 (m, 1H), 2.28-2.23 (m, 2H), 2.15-2.09 (m, 1H), 1.90-1.80 (m, 1H), 0.86 (s, 9H), 0.21 (s, 3H), 0.10 (s, 3H), −0.01 (s, 9H); ¹³C NMR (125 MHz, CDCl₃) δ 189.4, 181.5, 167.3, 149.5, 135.1, 128.7, 128.5, 128.4, 108.5, 104.8, 81.0, 72.3, 61.3, 54.9, 46.1, 41.9, 37.1, 31.1, 30.8, 26.1, 25.7, 21.8, 18.9, −0.4, −2.7, −3.6; FTIR (neat film), cm⁻¹ 2953 (w), 1721 (s), 1653 (w), 1614 (w), 1510 (s), 1472 (w), 1454 (w), 1254 (s), 1204 (w), 1150 (w), 1024 (w), 934 (s), 901 (s), 835 (s); HRMS-ESI (m/z): [M+H]⁺ calcd for C₃₃H₅₁N₂O₅S₂Si₂, 675.2772. Found, 675.2783.

Example 11 Synthesis of β-Methoxymethoxymethylenone 18

N-Bromosuccinimide (3.39 g, 19.0 mmol, 6.0 equiv) was added in one portion to a solution of the Michael addition product 17 (2.14 g, 3.17 mmol, 1 equiv) in tert-butanol (85 mL) and water (0.85 mL) at 23° C. The reaction mixture was stirred at this temperature for 100 min, then was partitioned between dichloromethane (300 mL) and saturated aqueous sodium bicarbonate solution (200 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (150 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, affording a yellow solid. The crude product was dissolved in diethyl ether (250 mL) and the resulting solution was washed with aqueous sodium hydroxide solution (0.5 M, 4×150 mL). The organic phase was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Sodium triacetoxyborohydride (2.62 g, 11.7 mmol, 3.7 equiv) was added to a solution of the crude product in benzene (20 mL) at 23° C. The resulting solution was heated to 40° C. After stirring at 40° C. for 4½ h, the reaction mixture was allowed to cool to 23° C. and the cooled solution was diluted with dichloromethane (100 mL). The resulting solution was added carefully to saturated aqueous sodium bicarbonate solution (100 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (100 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Chloromethyl methyl ether (446 μL, 5.87 mmol, 1.85 equiv) was added to a solution of the crude reduction product and N,N-diisopropylethylamine (2.04 mL, 11.7 mmol, 3.7 equiv) in benzene (10 mL) at 23° C. The reaction flask was sealed and the solution was heated to 50° C. After stirring at 50° C. for 6 h, the reaction mixture was allowed to cool to 23° C., and the cooled solution was partitioned between dichloromethane (100 mL) and saturated aqueous sodium bicarbonate solution (100 mL). The layers were separated and the aqueous phase was further extracted with dichloromethane (100 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by flash-column chromatography (15% ethyl acetate-hexanes, grading to 20% ethyl acetate-hexanes), affording the desired β-methoxymethoxymethylenone 18 as a yellow solid (875 mg, 50% yield, three steps). R_(f)=0.40 (30% ethyl acetate-hexanes); NMR (500 MHz, CDCl₃) δ 7.50 (d, 2H, J=7.0 Hz), 7.40-7.32 (m, 3H), 6.21 (s, 1H), 5.35 (AB quartet, 2H, J=12.0 Hz, Δν=2.0 Hz), 4.67 (AB quartet, 2H, J=7.0 Hz, Δν=4.5 Hz), 4.16 (m, 2H), 3.74 (d, 1H, J=10.0 Hz), 3.38 (s, 3H), 2.80-2.74 (m, 3H), 2.45 (s, 6H), 0.82 (s, 9H), 0.26 (s, 3H), 0.05 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 193.1, 187.7, 181.1, 167.5, 159.7, 135.0, 128.5, 128.5, 128.5, 122.4, 108.4, 96.0, 83.0, 72.6, 68.4, 59.6, 55.5, 47.5, 41.9, 25.9, 25.8, 19.0, −2.5, −4.1; FTIR (neat film), cm⁻¹ 2951 (w), 2930 (w), 1719 (s), 1674 (m), 1510 (s), 1175 (m), 1152 (m), 1038 (s), 934 (s), 829 (s), 735 (s); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₉H₄₁N₂O₇Si, 557.2678. Found, 557.2690.

Example 12 Synthesis of Michael-Claisen Cyclization Product 20

Cyclyzation Step: A freshly solution of lithium diisopropylamide (1.0 M, 7.86 mL, 7.86 mmol, 3.6 equiv) was added dropwise via syringe to a solution of the phenyl ester D-ring precursor 19 (2.84 g, 7.86 mmol, 3.6 equiv) and N,N′-tetramethylethylenediamine (2.27 mL, 15.1 mmol, 7 equiv) in tetrahydrofuran (60 mL) at −78° C., forming a bright red solution. After stirring at −78° C. for 40 min, a solution of the 13-methoxymethoxymethylenone 18 (1.20 g, 2.16 mmol, 1 equiv) in tetrahydrofuran (15 mL) was added dropwise via syringe to the reaction solution. The resulting mixture was allowed to warm slowly to −10° C. over 80 min, then was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 100 mL) and dichloromethane (100 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (2×75 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, affording an orange-yellow oil. The product was purified by flash-column chromatography (3.5% ethyl acetate-dichloromethane), providing the Michael-Claisen cyclization product 20 as a yellow solid (1.29 g, 72%). R_(f)=0.31 (30% ethyl acetate-hexanes); ¹H NMR (500 MHz, CDCl₃) δ 16.77 (s, 1H), 7.51 (brd, 4H, J=8.0 Hz), 7.41-7.28 (m, 6H), 7.21 (d, 1H, J=9.0 Hz), 6.90 (d, 1H, J=9.0 Hz), 5.38 (s, 2H), 5.17 (AB quartet, 2H, J=12.5 Hz, Δν=29.5 Hz), 4.47 (d, 1H, J=6.5 Hz), 4.34 (d, 1H, J=6.5 Hz), 4.15 (d, 1H, J=9.5 Hz), 3.78 (d, 1H, J=16.5 Hz), 3.38 (d, 1H, J=9.0 Hz), 3.27 (d, 1H, J=9.5 Hz), 3.12 (s, 3H), 2.63 (s, 6H), 2.65-2.58 (m, 1H), 2.51 (s, 6H), 2.51-2.41 (m, 2H), 2.32 (dd, 1H, J=14.5, 2.0 Hz), 0.93 (s, 9H), 0.29 (s, 3H), 0.20 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 186.9, 184.6, 183.0, 181.6, 167.7, 154.7, 145.7, 136.8, 136.1, 135.1, 128.5, 128.4, 128.4, 128.3, 127.7, 127.0, 125.0, 120.7, 113.7, 108.1, 107.2, 96.1, 82.3, 72.9, 72.4, 71.4, 61.1, 54.6, 46.4, 44.4, 41.9, 35.8, 34.7, 28.4, 26.5, 19.3, −2.0, −2.1; FTIR (neat film), 2932 (w), 1721 (s), 1611 (w), 1510 (m), 1472 (m), 1452 (m), 1269 (w), 1148 (w), 1107 (w), 1040 (s), 1020 (s), 922 (w), 831 (s), 733 (s) cm⁻¹; HRMS-ESI (m/z): [M+H]⁺ calcd for C₄₆H₅₈N₃O₉Si, 824.3937. Found, 824.3885.

Example 13 Synthesis of Alcohol 21

Deprotection Step: Perchloric acid (13.0 mL, 70% solution) was added dropwise over 5 min to a solution of the Michael-Claisen cyclization product (1.04 g, 1.26 mmol, 1 equiv) in tetrahydrofuran (130 mL) at 23° C. After stirring at this temperature for 10 min, the reaction solution was slowly and carefully poured into ice-cold saturated aqueous sodium bicarbonate solution (300 mL). The resulting mixture was extracted with dichloromethane (2×250 mL, then 50 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, providing an orange-yellow oil. The product was purified by flash-column chromatography (55% ethyl acetate-hexanes, grading to 75% ethyl acetate-hexanes), affording the desired alcohol 21 as a yellow solid (720 mg, 73%). R_(f)=0.26 (65% ethyl acetate-hexanes); ¹H NMR (500 MHz, CDCl₃) δ 16.76 (s, 1H), 7.53-7.49 (m, 4H), 7.41-7.28 (m, 6H), 7.22 (d, 1H, J=9.0 Hz), 6.90 (d, 1H, J=9.0 Hz), 5.38 (s, 2H), 5.17 (AB quartet, 2H, J=12.5 Hz, Δν=35 Hz), 4.11 (d, 1H, J=9.5 Hz), 3.66 (d, 1H, J=16.0 Hz), 3.48 (d, 1H, J=11.0 Hz), 3.32 (d, 1H, J=11.0 Hz), 2.64 (s, 6H), 2.68-2.59 (m, 1H), 2.56-2.48 (m, 1H), 2.51 (s, 6H), 2.38 (dd, 1H, J=14.5, 4.5 Hz), 2.23 (brd, 1H, J=14.0 Hz), 0.92 (s, 9H), 0.25 (s, 3H), 0.18 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 186.7, 184.7, 182.7, 181.4, 167.7, 154.9, 145.7, 136.8, 135.9, 135.1, 128.5, 128.5, 128.5, 128.3, 127.8, 126.9, 125.3, 120.7, 113.7, 108.2, 107.3, 82.3, 72.4, 71.4, 68.2, 61.3, 46.2, 44.7, 42.0, 36.8, 34.5, 28.2, 26.5, 19.3, −1.8, −2.0; FTIR (neat film), 2938 (w), 1719 (m), 1609 (w), 1510 (s), 1452 (s), 1265 (m), 1020 (m), 829 (s), 733 (s) cm⁻¹; HRMS-ESI (m/z): [M+H]⁺ calcd for C₄₄H₅₄N₃O₈Si, 780.3675. Found, 780.3654.

Example 14 Synthesis of Cyclopropane Intermediate 22

Cyclopropane Ring-Forming Step: 4 Å molecular sieves (2.4 g, small chunks) were added to a solution of the alcohol product 21 from the deprotection step above (720 mg, 0.923 mmol, 1 equiv) in dichloromethane (72 mL) and pyridine (7.2 mL) at 23° C. The resulting mixture was stirred at 23° C. for 1 h, then was cooled to 0° C. A solution of phosgene in toluene (20 wt %, 537 μL, 1.02 mmol, 1.1 equiv) was added to the cooled reaction mixture. After stirring at 0° C. for 1 h, aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 20 mL) was added to the reaction solution. The resulting mixture was allowed to warm to 23° C., then was filtered to remove 4 Å molecular sieves. Dichloromethane (60 mL) and aqueous potassium phosphate buffer solution (pH 7.0, 0.2M, 60 mL) were added and the phases were separated. The aqueous phase was further extracted with dichloromethane (2×60 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, providing an orange-yellow oil. The product was purified by flash-column chromatography (20% ethyl acetate-hexanes, grading to 30% ethyl acetate-hexanes), affording the cyclopropane 22 as a yellow solid (572 mg, 81%). R₁=0.25 (30% ethyl acetate-hexanes); ¹H NMR (500 MHz, CDCl₃) δ 7.53-7.24 (m, 10H), 7.13 (d, 1H, J=9.0 Hz), 6.86 (d, 1H, J=9.0 Hz), 5.35 (s, 2H), 5.05 (AB quartet, 2H, J=12.0 Hz, Δν=61.5 Hz), 4.01 (d, 1H, J=10.5 Hz), 3.85 (d, 1H, J=17.0 Hz), 2.77 (d, 1H, J=17.5 Hz), 2.68-2.57 (m, 3H), 2.62 (s, 6H), 2.49 (s, 6H), 2.25 (d, 1H, J=5.0 Hz), 1.71 (d, 1H, J=5.5 Hz), 0.89 (s. 9H), 0.28, (s, 3H), 0.12 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 194.4, 191.8, 185.3, 180.9, 167.6, 152.6, 144.8, 136.7, 135.0, 132.2, 128.6, 128.5, 128.5, 128.4, 127.6, 127.1, 123.3, 123.2, 113.5, 107.9, 84.0, 72.6, 71.2, 58.8, 49.0, 44.8, 43.1, 41.8, 32.1, 31.1, 30.9, 26.6, 26.3, 19.5, −2.0, −2.6; FTIR (neat film), 2938 (w), 1728 (s), 1711 (m), 1670 (w), 1510 (m), 1474 (m), 1452 (m), 1362 (w), 1258 (m), 916 (m), 827 (s), 733 (s) cm⁻¹; HRMS-ESI (m/z): [M+H]⁺ calcd for C₄₄H₅₂N₃O₇Si, 762.3569. Found, 762.3569.

Example 15 Synthesis of Azide 22

Sodium azide (12.8 mg, 0.197 mmol, 3.0 equiv) was added to a solution of the cyclopropane 22 (50 mg, 0.066 mmol, 1 equiv) in dimethylformamide (2.0 mL) at 23° C. The resulting solution was stirred for 12 h, then was partitioned between a saturated aqueous sodium chloride solution (20 mL) and diethyl ether (20 mL). The phases were separated and the aqueous phase was further extracted with diethyl ether (20 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by flash-column chromatography (12% ethyl acetate-hexanes), providing the alkyl azide 23 as a yellow solid (40 mg, 75%). R_(f)=0.41 (30% ethyl acetate-hexanes); ¹H NMR (500 MHz, CDCl₃) δ 16.72 (s, 1H), 7.51 (brd, 4H, J=8.0 Hz), 7.41-7.26 (m, 7H), 6.95 (d, 1H, 8.5 Hz), 5.38 (s, 2H), 5.18 (AB quartet, 2H, J=12.5 Hz, Δν=36.5 Hz), 4.11 (d, 1H, J=10.5 Hz), 3.72 (d, 1H, J=16.5 Hz), 3.30 (d, 1H, J=11.5 Hz), 3.13 (d, 1H, J=11.5 Hz), 2.65 (s, 6H), 2.65-2.45 (m, 2H), 2.51 (s, 6H), 2.35-2.25 (m, 2H), 0.92 (s, 9H), 0.27 (s, 3H), 0.19 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 186.5, 184.0, 183.6, 181.5, 167.7, 154.9, 145.9, 136.7, 135.3, 135.0, 128.5, 128.5, 128.5, 128.4, 127.9, 127.0, 125.8, 120.2, 114.0, 108.3, 107.3, 82.3, 72.5, 71.5, 61.1, 59.1, 46.6, 44.6, 41.9, 36.4, 35.2, 28.3, 26.5, 19.3, −1.9, −2.1; HRMS-ESI (m/z): [M+H]⁺ calcd for C₄₄H₅₃N₆O₇Si, 805.3740. Found, 805.3846.

Example 16 Synthesis of C5a-n-Butoxymethylminocycline 24

Anhydrous magnesium bromide (7.2 mg, 0.039 mmol, 2.0 equiv) was added to a solution of the cyclopropane 22 (15.0 mg, 0.020 mmol, 1 equiv) in n-butanol (1.0 mL) at 23° C. The resulting mixture was heated to 75° C. After stirring at 75° C. for 14 h, the reaction solution was allowed to cool to 23° C. The cooled solution was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 10 mL) and dichloromethane (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 13½ h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.8 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 3¾ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μM, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 41-44 min were collected and concentrated, affording C5a-n-butoxymethylminocycline trifluoroacetate 24 as a yellow solid (7.3 mg, 56%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.81 (d, 1H, J=9.0 Hz), 7.04 (d, 1H, J=9.6 Hz), 4.16 (s, 1H), 3.50 (d, 1H, J=10.2 Hz), 3.38-3.30 (m, 3H), 3.21 (d, 1H, J=9.6 Hz), 3.13 (s, 6H), 3.11-3.06 (m, 1H), 2.98 (s, 6H), 2.58 (d, 1H, J=15.6 Hz), 2.42 (dd, 1H, J=13.8, 3.0 Hz), 1.71 (t, 1H, J=13.8 Hz), 1.50-1.39 (m, 2H), 1.34-1.24 (m, 2H), 0.87 (t, 3H, J=7.2 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₈H₃₈N₃O₈, 544.2653. Found, 544.2655.

Example 17 Synthesis of C5a-Hydroxymethylminocycline 25

Concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added to a solution of the alcohol 21 formed from Example 13 (10.0 mg, 0.013 mmol, 1 equiv) in acetonitrile (0.8 mL) in a polypropylene reaction vessel at 23° C. The reaction solution was stirred vigorously at 23° C. for 25 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, affording an orange-yellow oil. Methanol (1.5 mL) and dioxane (1.5 mL) were added to the crude product, forming an orange-yellow solution. Palladium black (3.2 mg, 0.030 mmol, 2.3 equiv) was added in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1½ h, then was filtered through a plug of Celite. The filtrate was concentrated, affording a yellow solid. The product was purified by preparatory HPLC on a Phenomenex Polymerx DVB column [7 μm, 150×21.2 mm, UV detection at 350 nm, Solvent A: 0.05 N aq. HCl, Solvent B: acetonitrile, crude product co-injected with 10 mg oxalic acid and 500 μL methanol, gradient elution with 5→30% B over 50 min, flow rate: 6 mL/min]. Fractions eluting at 16-22 min were collected and concentrated, affording 5a-hydroxymethylminocycline hydrochloride 25 as a yellow solid (3.1 mg, 46%, two steps). NMR (600 MHz, CD₃OD, hydrochloride) δ 7.93 (d, 1H, J=9.6 Hz), 7.09 (d, 1H, J=9.0 Hz), 4.18 (s, 1H), 3.67 (d, 1H, J=12.0 Hz), 3.41 (d, 1H, J=15.6 Hz), 3.40-3.27 (m, 6H), 3.23 (d, 1H, J=11.4 Hz), 3.13-3.02 (m, 7H), 2.62 (d, 1H, J=15.6 Hz), 2.48 (dd, 1H, J=13.8, 2.4 Hz), 1.68 (brt, 1H, J=13.8 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₄H₃₀N₃O₈, 488.2027. Found, 488.2029.

Example 18 Synthesis of C5a-Methoxymethylminocycline 27

Anhydrous magnesium bromide (1.7 mg, 0.009 mmol, 1 equiv) was added to a solution of the cyclopropane 26 (7.0 mg, 0.009 mmol, 1 equiv) in methanol (1.0 mL) at 23° C. The resulting mixture was heated to 55° C. After stirring at 55° C. for 24 h, the reaction solution was allowed to cool to 23° C. The cooled solution was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 10 mL) and dichloromethane (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (0.7 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 1.0 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 22 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (7.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (2.7 mg, 0.025 mmol, 2.8 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 10 min, then was filtered through a plug of Celite. The filtrate was concentrated, providing a yellow-brown oil. The product was purified by preparatory HPLC on a Phenomenex Polymerx DVB column [7 vim, 150×21.2 mm, UV detection at 350 nm, Solvent A: 0.05 N aq. HCl, Solvent B: acetonitrile, crude product co-injected with 10 mg oxalic acid and 500 μL methanol, gradient elution with 5→30% B over 50 min, flow rate: 6 mL/min]. Fractions eluting at 21-25 min were collected and concentrated, affording C5a-methoxymethylminocycline hydrochloride 27 as a yellow solid (2.5 mg, 52%, three steps). ¹H NMR (600 MHz, CD₃OD, hydrochloride) δ 7.90 (d, 1H, J=9.0 Hz), 7.09 (d, 1H, J=9.6 Hz), 4.18 (s, 1H), 3.51 (d, 1H, J=10.2 Hz), 3.36-3.21 (m, 7H), 3.26 (s, 3H), 3.13 (d, 1H, J=9.6 Hz), 3.06 (brd, 1H, J=13.2 Hz), 3.02 (brs, 3H), 2.98 (brs, 3H), 2.63 (brd, 1H, J=17.4 Hz), 2.44 (dd, 1H, J=14.4, 3.0 Hz), 1.71 (t, 1H, J=14.4 Hz).

Example 19 Synthesis of 5-Dimethylphenylcyclopentadiene

The following experimental procedure was based on literature precedent (Landais, Y.; Rapadp, P. Eur. J. Org. Chem. 2000, 401-418). n-Butyllithium (2.5 M solution in hexane, 230 mL, 576 mmol, 1 equiv) was added dropwise by cannula over 20 min to a dry ice-acetone cooled solution of freshly cracked cyclopentadiene (38.1 g, 576 mmol, 1 equiv) in tetrahydrofuran (576 mL). The resulting white slurry was stirred for 45 min, whereupon dimethylphenylchlorosilane (98.3 g, 576 mmol, 1 equiv) was added dropwise by cannula over 20 min. After 1.5 h, saturated aqueous ammonium chloride solution (100 mL) and water (100 mL) were added sequentially. The dry ice-acetone cooling bath was replaced with a 23° C. water bath and the mixture was stirred for 20 min. The product solution was transferred to a four liter separation funnel containing water (400 mL) and diethyl ether (400 mL). The layers were separated. The aqueous layer was extracted with diethyl ether (200 mL). The organic layers were combined and the combined solution was washed with saturated aqueous sodium chloride solution (200 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated first by rotary evaporation (23° C., 40 mmHg) for 45 min then on a high vacuum manifold (23° C., 0.1 mmHg) for 2 h to provide 5-dimethylphenylcyclopentadiene as a pale-yellow liquid (116 g, 101%) which was stored as a off-white solid in a −80° C. fridge. No further purification was conducted.

Example 20 Synthesis of Meso-Diol 28

5-Diemthylphenylcyclopentadiene was removed from an −80° C. fridge and allowed to warm to 23° C. (see Example 19). An ice-water cooled solution of 5-dimethylphenylcyclopentadiene (−124 g, 586 mmol, 1 equiv) in methanol-dichloromethane (2:1, 200 mL) was added dropwise by cannula over 30 min to an ice-water cooled solution of p-benzoquinone (recrystallized from hot ethanol, 63.3 g, 586 mmol, 1 equiv) in methanol-dichloromethane (2:1, 1200 mL). The resulting dark amber solution was stirred for 12 h while maintaining the internal temperature of the reaction <5° C., whereupon cerium trichloride heptahydrate (109 g, 293 mmol, 0.5 equiv) was added in 25 g portions over 10 min. The resulting slurry was stirred for 15 min. Sodium borohydride (22.2 g, 586 mmol, 1 equiv) was added in 1 g portions over 45 min. After 10 min the product mixture was concentrated to half-volume by rotary evaporation (27° C., 40 mmHg). Ethyl acetate (500 mL) was added and the solution filtered through a 1 inch pad of silica gel rinsing with ethyl acetate (1 L). Aqueous citric acid solution (1M, 250 mL) was added to the filtrate with stirring. After 15 min the biphasic mixture was transferred to a 6-L separation funnel containing aqueous citric acid solution (750 mL) and ethyl acetate (1 L). The layers were separated. The organic layer was washed sequentially with water (2×500 mL), 1 M aqueous sodium carbonate solution containing 10% by volume 1 M aqueous sodium sulfite solution (3×500 mL), then saturated aqueous sodium chloride solution (500 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide a light yellow solid (158 g). The crude solid was dissolved in boiling dichloromethane (350 mL) then hot (60° C.) hexanes (900 mL) was added slowly over 10 min with stirring. The solution was allowed to slowly cool to 23° C. during which time a white crystalline solid formed. The mixture was further cooled in a ice-water bath for 1 h. The mixture was filtered and the filter cake washed with ice-water cooled hexanes to provide the meso-diol 28 as a white crystalline solid (129 g, 70%). ¹H NMR (600 MHz, CDCl₃) δ: 7.45-7.43 (m, 2H), 7.33-7.31 (m, 3H), 5.82 (s, 2H), 5.55 (s, 2H), 4.41-4.39 (m, 2H), 3.11 (s, 2H), 2.79-2.78 (m, 2H), 1.63 (d, 2H, J=5.6 Hz), 1.23 (s, 1H), 0.21 (s, 6H); ¹³C NMR (125 MHz, CDCl₃) δ: 140.2, 135.0, 133.5, 131.9, 128.5, 127.6, 66.7, 51.7, 47.8, 45.2, −1.3; FTIR (neat), cm⁻¹: 3383 (br), 2967 (w), 2911 (w).

Example 21 Synthesis of Mono-Acetate 29

A 5-liter, 3-neck round bottom flask equipped with an overhead mechanical stirrer, a nitrogen-inlet, and a rubber septum was charged with meso-diol 28 (150 g, 480 mmol, 1 equiv) and triethylamine (1.6 L). The mixture was stirred resulting in a light-brown homogeneous solution. Isopropenyl acetate (168 g, 1680 mmol, 3.5 equiv) was added, then the lipase (Amano “PS” 1M, 150 g). The resulting slurry was stirred for 20 h at 23° C. and then filtered through a sintered-glass funnel, rinsing with ethyl acetate (1 L). The filtrate was concentrated to afford a dark brown liquid which was dissolved in ethyl acetate (1.5 L) and transferred to a 4 L separation funnel. The organic product solution was wash sequentially with saturated aqueous ammonium chloride solution (800 mL), saturated aqueous sodium bicarbonate solution (800 mL), and saturated aqueous sodium chloride solution (800 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide an off-white solid (161 g, 95%). The product was dissolved with ethyl acetate (1.2 L) and charcoal (32 g, Darco G-60) was added. The resulting black heterogeneous mixture was stirred at 50° C. for 60 min and then cooled to 23° C. The mixture was filtered through a 2 in pad of Celite rinsing with ethyl acetate. The filtrate was concentrated to a white solid (159 g, 94%) to yield mono-Acetate 29. ¹H NMR (600 MHz, CDCl₃) δ: 7.44-7.42 (m, 2H), 7.33-7.31 (m, 3H), 5.76 (dd, 1H, J=2.8, 5.4 Hz), 5.69 (dd, 1H, J=2.8, 5.4 Hz), 5.43-5.40 (m, 1H), 5.38-5.35 (m, 1H), 5.27-5.24 (m, 1H), 4.78-4.44 (m, 1H), 3.14 (s, 1H), 3.03-2.99 (m, 1H), 2.91 (s, 1H), 2.87-2.84 (m, 1H), 2.11 (s, 3H), 1.52 (d, 1H, J=6.1 Hz), 1.17 (s, 1H), 0.19 (s, 3H), 0.18 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ: 170.7, 140.1, 135.3, 135.1, 133.5, 131.8, 128.5, 127.6, 126.7, 70.1, 66.7, 50.4, 48.5, 47.8, 44.0, 40.8, 21.1, −1.3, −1.4; FTIR (neat), cm⁻¹: 3455 (br), 3067 (w), 2967 (w), 1738 (s), 1371 (s), 1246 (s); HRMS (ESI): Calcd for (C₂₁H₂₆O₃Si+Na)⁺ 377.1543, found 377.1544.

Example 22 Synthesis of Enone 30

Ammonium formate (48 g, 0.760 mmol, 1.5 equiv) was added in one portion to a stirring solution of mono-acetate 29 (180 g, 0.510 mmol, 1 equiv) in dimethylformamide (1.3 L) and water (100 mL) at 23° C. The resulting solution was degassed by bubbling argon gas for 40 min, whereupon Pd(dppf)₂Cl₂ (16.9 g, 0.020 mmol, 0.04 equiv) was added in one portion. The resulting reaction mixture was stirred at 23° C. for 16 h. The reaction was cooled to −20° C., then methyl tert-butyl ether (500 mL), water (250 mL), and charcoal (36 g, Darco® G-60) was added. The resulting slurry was stirred at −10° C. for 1 h. The product mixture was filtered through a 2-L sintered glass funnel containing Celite, rinsing with methyl tert-butyl ether. Water (500 mL) was added to the filtrate and the layers were separated. The organic layer was washed with saturated aqueous sodium chloride solution (4×300 mL), saturated aqueous sodium bicarbonate solution (2×300 mL), and water (300 mL). The washed solution was dried over magnesium sulfate and the dried solution was filtered. The filtered solution was concentrated to provide a brown solid (135 g). The solid was dissolved in methyl tert-butyl ether (1 L) then MP-TMT resin (73 g, Biotage) was added. The resulting slurry was stirred at 23° C. for 16 h then filtered through a sintered glass funnel rinsing with methyl tert-butyl ether. The filtrate was concentrated to provide enone 30 as an orange solid (124 g, 82%) which was used in the next step (Example 23) without any further purification. ¹H NMR (500 MHz, CDCl₃) δ: 7.44-7.42 (m, 2H), 7.34-7.32 (m, 3H), 6.63 (ddd, 1H, J=4.1, 4.1, 10.3 Hz), 6.03 (dd, 1H, J=2.8, 5.6 Hz), 5.98 (dd, 1H, J=2.9, 5.7 Hz), 5.84 (ddd, 1H, J=2.3, 2.3, 10.3 Hz), 3.50-3.48 (m, 1H), 3.09-3.07 (m, 1H), 2.92 (dd, 1H, J=4.0, 9.8 Hz), 2.74 (dddd, 1H, J=3.5, 3.5, 10.3, 10.3), 2.55 (dddd, 1H, J=2.6, 3.8, 10.5, 20.9 Hz), 2.01-1.96 (m, 1H), 1.21 (s, 1H), 0.21 (s, 3H), 0.20 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ: 200.8, 149.6, 139.9, 137.5, 134.5, 133.8, 129.4, 129.0, 128.0, 52.3, 51.9, 51.4, 50.8, 36.5, 27.7, −1.22, −1.23.

Example 23 Synthesis of Michael-Claisen Cyclization Product 33

A 5-liter, 3-neck, round-bottom flask equipped with an overhead mechanical stirrer, an argon inlet, and a rubber septum was charged with a solution of methyl ester 32 (134 g, 462 mmol, 1.1 equiv) in tetrahydrofuran (1.2 L). The resulting yellow solution was cooled to −50° C. in a dry ice-acetone bath, whereupon a solution of NaHMDS (93.2 g, 483 mmol, 1.15 equiv) in tetrahydrofuran (500 mL) was added dropwise by cannula over 30 min. The resulting mixture was stirred at −50° C. for 1 h during which time a fine off-white suspension was observed. A solution of enone 31 (124 g, 421 mmol, 1 equiv) in tetrahydrofuran (200 mL) was added dropwise by cannula over 40 min and the resulting mixture stirred for 1 h at −50° C., whereupon a solution of KHMDS (88 g, 421 mmol, 1 equiv) in tetrahydrofuran (420 mL) was added dropwise by cannula over 30 min. The resulting solution was warmed to −20° C. over the course of 1 h then held at this temperature for 2 h. The reaction mixture was warmed to −10° C. over 20 min and held at this temperature for 2 h, and then water (300 mL) was added and the cooling bath was removed. The tetrahydrofuran was removed by rotary evaporation then ethyl acetate (1 L) and water (500 mL) was added. The biphasic mixture was separated and the aqueous layer was extracted with ethyl acetate (2×500 mL). The organic layers were combined and the combined solution was dried over magnesium sulfate. The dried solution was filtered and the filtrate was concentrated to afford a brown foam. The residue was dissolved with methyl tert-butyl ether (1.2 L) and transferred to a 3-liter, 3-neck, round-bottom flask equipped with an overhead mechanical stirrer. The solution was cooled in an ice-water bath then a solution of hydrochloric acid in ether (2 N, 260 mL, 520 mmol, 1.24 equiv) was added dropwise by syringe over 30 min. The resulting slurry was stirred for 1 h then filtered. The filter cake was washed with methyl tert-butyl ether (2×500 mL) and ethyl ether (500 mL) then dried on a high vacuum manifold (0.1 mmHg) at 23° C. to provide the hydrochloride salt of 33 (250 g) as an orange solid. This solid was separated into two equal portions (−125 g each) and each portion was dissolved in dichloromethane (700 mL). Ethyl acetate (400 mL) was added to each portion. An off-white solid began to crash out of each solution. The slurry was concentrated to a volume of 800 mL on a rotary evaporator then filtered through a sintered glass funnel. The filter cake was rinsed with ethyl acetate (2×400 mL) and the two filter cakes were combined and dried on a high vacuum manifold (0.1 mmHg, 23° C.) to afford the hydrochloride salt of 33 as an off-white solid (155 g).

The mother liquor from above was concentrated and then dissolved with dichloromethane (800 mL). This solution was washed with a 1 M aqueous dipotassium hydrogen phosphate solution (2×400 mL) and then a saturated aqueous sodium chloride solution (400 mL). The washed solution was dried over magnesium sulfate. The dried solution was filtered and the filtrate was concentrated to provide a brown oil (85 g). This oil was dissolved with dichloromethane (75 mL) then filtered through a pad of neutral alumina rinsing with 20% ethyl acetate-hexanes. The filtrate was concentrated to afford an orange oil (25 g) which was dissolved in ethyl ether (226 mL) then cooled in an ice-water bath. A 2 N solution of hydrochloric acid in ethyl ether (23 mL) was added. The resulting slurry was stirred for 30 min then filtered through a sintered glass funnel. The filter cake was rinsed with ethyl ether then dried on a high vacuum manifold to afford an off-white solid. This solid was dissolved in dichloromethane (200 mL) and ethyl acetate (150 mL), and this solution was concentrated to a volume of 150 mL at which point an off-white solid began to crash out. This slurry was filtered through a sintered glass funnel and the filter cake was rinsed with ethyl acetate, and then dried on a high vacuum manifold to provide the hydrochloride salt of 33 as an off-white solid (10 g). Total weight=155 g+10 g=165 g. This solid was recrystallized from dichloromethane-ethyl acetate and washed with 1 M aqueous dipotassium hydrogen phosphate solution to provide 33 (146 g, 62%) as a white foam. ¹H NMR (500 MHz, CDCl₃) δ: 15.1 (s, 1H), 7.52-7.50 (m, 2H), 7.47-7.28 (m, 8H), 5.92 (t, 2H, J=1.4 Hz), 5.37 (s, 2H), 3.59 (d, 1H, J=6.8 Hz), 3.32 (s, 1H), 2.98 (s, 1H), 2.91-2.88 (m, 1H), 2.76-2.69 (m, 2H), 2.17-2.08 (m, 1H), 2.13 (s, 6H), 1.78 (dd, 1H, J=4.8, 15.1 Hz), 1.35 (s, 1H), 0.20 (s, 3H), 0.19 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ: 184.2, 181.0, 168.0, 139.9, 135.6, 135.5, 133.8, 129.0, 128.8, 128.7, 127.9, 108.3, 105.7, 72.6, 58.6, 53.8, 52.8, 50.1, 45.4, 40.4, 34.6, 26.7, −1.24.

Example 24 Synthesis of C5a-Methylminocycline 37

Cyclization Step. A freshly prepared solution of lithium diisopropylamide in tetrahydrofuran (1.0 M, 121 μL, 0.121 mmol, 3.0 equiv) was added dropwise via syringe to a solution of phenyl ester 34 (45 mg, 0.121 mmol, 3.0 equiv) and TMEDA (36 μL, 0.240 mmol, 6.0 equiv) in tetrahydrofuran (2.0 mL) at −78° C., forming a bright red solution. After stirring at −78° C. for 40 min, a solution of the AB enone 35 (20.0 mg, 0.040 mmol, 1 equiv) in tetrahydrofuran (1.5 ml) was added dropwise via syringe to the reaction solution. The resulting mixture was allowed to warm slowly to −10° C. over 80 min, then was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 5 mL) and dichloromethane (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (2×10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, affording a yellow oil. The product was purified by preparatory HPLC on a Coulter Ultrasphere ODS column [5 μM, 10 mm×25 cm, UV detection at 350 nm, Solvent A: water, Solvent B: methanol, injection volume: 500 μL (methanol), gradient elution 85-100% B over 60 min, flow rate 3.5 mL/min]. Fractions eluting at 40-48 min were collected and concentrated, affording the Michael-Claisen cyclization product 36 as a yellow oil (21.5 mg, 69%). R_(f)=0.28 (20% ethyl acetate-hexanes); ¹H NMR (600 MHz, CDCl₃) δ 15.96 (s, 1H, enol-OH), 7.49 (d, 2H, J=7.8 Hz, OCH₂ArH), 7.39-7.33 (m, 3H, OCH₂ArH), 7.26-7.24 (m, 1H, ArH), 7.04 (d, 1H, J=8.5 Hz, ArH), 5.36 (s, 2H, OCH₂Ph), 4.16 (d, 1H, J=10.0 Hz, CHN(CH₃)₂), 3.20 (d, 1H, J=16.1 Hz, CHH′C═CN(CH₃)₂), 2.75 (d, 1H, J=16.1 Hz, CHH′C═CN(CH₃)₂), 2.66 (s, 6H, ArC—N(CH₃)₂), 2.54-2.50 (m, 7H, CHN(CH₃)₂, CHCHN(CH₃)₂), 2.37 (d, 1H, J=14.4 Hz, CHH′CHCHN(CH₃)₂), 2.16 (d, 1H, J=14.8, 4.5 Hz, CHH′CHCHN(CH₃)₂), 1.56 (s, 9H, O—C(CH₃)₃), 1.12 (s, 3H, CH₃), 0.90 (s, 9H, Si—C(CH₃)₃), 0.25 (s, 3H, Si—CH₃), 0.21 (s, 3H, Si—CH₃); ¹³C NMR (125 MHz, CDCl₃) δ 186.8, 185.6, 181.7, 178.3, 167.6, 152.3, 150.4, 145.4, 136.4, 135.1, 128.5, 128.4, 128.3, 124.2, 123.9, 122.3, 112.0, 108.1, 83.8, 81.7, 72.4, 60.7, 47.0, 44.2, 41.9, 40.6, 32.4, 32.1, 29.8, 27.7, 26.4, 19.2, −1.9, −2.3; FTIR (neat film), cm⁻¹ 2959, 2936, 1759, 1721, 1613, 1510, 1474, 1456, 1370, 1310, 1285, 1265, 1236, 1152, 831, 737, 704; UV max (0.01 M methanolic HCl), nm 245, 275, 315; HRMS-ESI (m/z): [M+H]⁺ calcd for C₄₂H₅₅N₃O₉Si, 774.3780. Found, 774.3796.

Deprotection Steps. Concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added to a solution of the HPLC-purified product 36 from the cyclization step above (10.0 mg, 0.013 mmol, 1 equiv) in acetonitrile (0.8 mL) in a polypropylene reaction vessel at 23° C. The reaction solution was stirred vigorously at 23° C. for 23 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, affording an orange-yellow oil. Methanol (1.5 mL) and dioxane (1.5 mL) were added to the crude product, forming an orange-yellow solution. Palladium black (3.2 mg, 0.030 mmol, 2.3 equiv) was added in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 5 min, then was filtered through a plug of Celite. The filtrate was concentrated, affording a yellow solid. The product was purified by preparatory HPLC on a Phenomenex Polymerx DVB column [7 μm, 150×21.2 mm, UV detection at 350 nm, Solvent A: 0.05 N aq. HCl, Solvent B: acetonitrile, crude product co-injected with 10 mg oxalic acid and 500 μL methanol, gradient elution with 5→430% B over 50 min, flow rate: 6 mL/min]. Fractions eluting at 19-26 min were collected and concentrated, affording 5a-methylminocycline 37 as a yellow solid (3.1 mg, 51%, two steps). ¹H NMR (600 MHz, CD₃OD, hydrochloride) δ 7.94 (d, 1H, J=9.6 Hz), 7.10 (d, 1H, J=9.6 Hz), 4.18 (s, 1H), 3.35-3.22 (m, 6H), 3.09-3.00 (m, 2H), 3.06 (s, 3H), 3.01 (s, 3H), 2.83 (d, 1H, J=15.0 Hz), 2.13 (dd, 1H, J=13.8, 3.0 Hz), 1.95 (brt, 1H, J=13.8 Hz), 1.31 (s, 3H); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₄H₂₉N₃O₇, 472.2078. Found, 472.2087.

Example 25 Synthesis of C5a-Morpholinomethylminocycline 38

Anhydrous magnesium bromide (6.3 mg, 0.034 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (13.0 mg, 0.017 mmol, 1 equiv) and morpholine (15 μL, 0.17 mmol, 10 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 55° C. After stirring at 55° C. for 14 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was diluted with dichloromethane (10 mL) and saturated aqueous sodium bicarbonate solution (10 mL) was added. The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 16½ h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.8 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1¾ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→25% B over 50 min, then 25→100% B over 20 min, flow rate: 7.5 mL/min]. Fractions eluting at 49-52 min were collected and concentrated, affording C5a-morpholinomethylminocycline trifluoroacetate 38 as an orange-yellow solid (7.5 mg, 66%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.56 (d, 1H, J=9.0 Hz), 6.95 (d, 1H, J=9.0 Hz), 4.04 (s, 1H), 3.77-3.69 (m, 4H), 3.53 (d, 1H, J=16.8 Hz), 3.24 (brd, 1H, J=13.2 Hz), 3.18-3.14 (m, 1H), 3.08 (s, 6H), 2.99-2.94 (m, 2H), 2.88 (brd, 1H, J=15.0 Hz), 2.81-2.72 (m, 2H), 2.74 (s, 6H), 2.62 (d, 1H, J=16.8 Hz), 2.53 (brd, 1H, J=14.4 Hz), 1.92 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₈H₃₇N₄O₈, 557.2606. Found, 557.2611.

Example 26 Synthesis of C5a-piperazinylmethylminocycline 39

Anhydrous magnesium bromide (51.0 mg, 0.276 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (105 mg, 0.138 mmol, 1 equiv) and tert-butyl 1-piperazine carboxylate (186 mg, 1.00 mmol, 7.2 equiv) in tetrahydrofuran (2.0 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 45° C. After stirring at 45° C. for 36 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was diluted with dichloromethane (25 mL) and saturated aqueous sodium bicarbonate solution (25 mL) was added. The phases were separated and the aqueous phase was further extracted with dichloromethane (25 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product mixture was filtered through a short pad of silica gel (eluting with 40% ethyl acetate-hexanes) and the filtrate was concentrated, affording an orange-yellow oil. Methanol (2.5 mL) and dioxane (2.5 mL) were added to the crude product of cyclopropane ring-opening, forming an orange-yellow solution. Palladium black (25 mg, 0.235 mmol, 1.7 equiv) was added in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 2 h, then was filtered through a plug of Celite. The filtrate was concentrated, providing an orange solid. Concentrated aqueous hydrofluoric acid (48 wt %, 1.5 mL) was added to a solution of the crude product in acetonitrile (2.0 mL) in a polypropylene reaction vessel at 23° C. The reaction mixture was stirred vigorously at 23° C. for 14 h. Excess hydrofluoric acid was quenched by the careful addition of methoxytrimethylsilane (10.0 mL). The resulting mixture was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, 2 batches, injection volume (for each batch): 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→35% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 22-29 min were collected and concentrated, affording C5a-piperazinylmethylminocycline trifluoroacetate 39 as a yellow solid (63 mg, 68%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.58 (d, 1H, J=9.6 Hz), 6.93 (d, 1H, J=9.0 Hz), 4.06 (s, 1H), 3.44 (d, 1H, J=16.2 Hz), 3.11 (brd, 1H, J=12.6 Hz), 3.08-3.02 (m, 2H), 3.05 (s, 6H), 3.01-2.95 (m, 2H), 2.82 (s, 6H), 2.61-2.56 (m, 3H), 2.50 (d, 1H, J=16.2 Hz), 2.48-2.42 (m, 3H), 2.20 (dd, 1H, J=13.8, 3.0 Hz), 1.74 (t, 1H, J=13.8 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₃H₃₈N₅O₇, 556.2766. Found, 556.2771.

Example 27 Synthesis of C5a-Pyrrolidinomethylminocycline 40

Anhydrous magnesium bromide (8.2 mg, 0.045 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (17.0 mg, 0.022 mmol, 1 equiv) and pyrrolidine (18 μL, 0.223 mmol, 10 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction solution was stirred at 23° C. for 16 h, then was partitioned between dichloromethane (10 mL) and saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 20 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.1 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1¼ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→35% B over 50 min, then 25→100% B over 20 min,

flow rate: 7.5 mL/min]. Fractions eluting at 39-43 min were collected and concentrated, affording C5a-pyrrolidinomethylminocycline trifluoroacetate 40 as a yellow solid (12.5 mg, 86%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.55 (d, 1H, J=9.0 Hz), 6.95 (d, 1H, J=9.0 Hz), 4.05 (s, 1H), 3.84 (brs, 1H), 3.73 (d, 2H, J=14.4 Hz), 3.62 (d, 1H, J=16.8 Hz), 3.20 (d, 1H, J=13.2 Hz), 3.14 (d, 1H, J=15.0 Hz), 3.13-3.03 (m, 1H), 3.10 (s, 6H), 2.70 (s, 6H), 2.67 (d, 1H, J=16.8 Hz), 2.59 (dd, 1H, J=15.0, 3.0 Hz), 2.50 (brs, 1H), 2.02-1.90 (m, 5H); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₈H₃₇N₄O₇, 541.2657. Found, 541.2684.

Example 28 Synthesis of C5a-Piperidinylmethylminocycline 41

Anhydrous magnesium bromide (8.2 mg, 0.045 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (17.0 mg, 0.022 mmol, 1 equiv) and piperidine (22 μL, 0.223 mmol, 10 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction solution was stirred at 23° C. for 21 h, then was heated to 45° C. After stirring at this temperature for 14 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (15 mL) and saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 13 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.1 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1¼ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→435% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 40-44 min were collected and concentrated, affording C5a-piperidinylmethylminocycline trifluoroacetate 41 as a yellow solid (12.0 mg, 81%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.56 (d, 1H, J=9.0 Hz), 6.96 (d, 1H, J=9.0 Hz), 4.10 (d, 1H, J=2.4 Hz), 3.66 (d, 1H, J=16.8 Hz), 3.46 (d, 1H, J=14.4 Hz), 3.40-3.35 (brm, 1H), 3.27-3.23 (m, 1H), 3.23-3.18 (m, 1H), 3.10 (s, 6H), 3.10-3.00 (m, 2H), 2.71 (s, 6H), 2.71-2.62 (m, 2H), 2.59 (dd, 1H, J=15.0, 3.0 Hz), 2.02 (t, 1H, J=15.0 Hz), 1.95-1.88 (brm, 1H), 1.85-1.78 (brm, 2H), 1.72-1.61 (brm, 2H), 1.43-1.36 (brm, 1H); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₉H₃₉N₄O₇, 555.2813. Found, 555.2788.

Example 29 Synthesis of C5a-Cyclopropylaminomethylminocycline 42

Anhydrous magnesium bromide (8.2 mg, 0.045 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (17.0 mg, 0.022 mmol, 1 equiv) and cyclopropylamine (15 μL, 0.223 mmol, 10 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was stirred at 23° C. for 16 h, then was heated to 40° C. After stirring at this temperature for 22 h, more cyclopropylamine (15 μL, 0.223 mmol, 10 equiv) was added to the reaction mixture. The flask was re-sealed and the reaction solution was stirred at 40° C. for a further 13 h, then was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (15 mL) and saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 12 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.1 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 3½ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→35% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 35-36 min were collected and concentrated, affording C5a-cyclopropylaminomethylminocycline trifluoroacetate 42 as a yellow solid (3.0 mg, 21%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.58 (d, 1H, J=9.0 Hz), 6.96 (d, 1H, J=9.0 Hz), 4.00 (d, 1H, J=2.4 Hz), 3.60 (d, 1H, J=14.4 Hz), 3.55 (d, 1H, J=16.8 Hz), 3.19-3.10 (m, 1H), 3.13 (s, 6H), 3.03 (d, 1H, J=14.4 Hz), 2.76 (s, 6H), 2.76-2.70 (m, 1H), 2.62-2.58 (m, 1H), 2.25 (dd, 1H, J=15.0, 3.0 Hz), 1.98 (t, 1H, J=13.8 Hz), 0.89-0.82 (m, 1H), 0.77-0.69 (m, 3H); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₇H₃₅N₄O₇, 527.2500. Found, 527.2502.

Example 30 Synthesis of C5a-Diethylaminomethylminocycline 43

Anhydrous magnesium bromide (7.2 mg, 0.039 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (15.0 mg, 0.020 mmol, 1 equiv) and diethylamine (102 μL, 0.987 mmol, 50 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 45° C. After stirring at this temperature for 20 h, more diethylamine (204 μL, 1.97 mmol, 100 equiv) was added to the reaction mixture. The flask was re-sealed and the reaction solution was stirred at 45° C. for a further 55 h, then was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (10 mL) and saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 10½ h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.4 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1¾ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 36-39 min were collected and concentrated, affording C5a-diethylaminomethylminocycline trifluoroacetate 43 as a yellow solid (12.0 mg, 93%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.54 (d, 1H, J=9.0 Hz), 6.95 (d, 1H, J=9.0 Hz), 4.10 (d, 1H, J=3.0 Hz), 3.61 (d, 1H, J=16.8 Hz), 3.42 (d, 1H, J=15.0 Hz), 3.25-3.20 (m, 2H), 3.16-3.02 (brm, 3H), 3.10 (s, 6H), 2.93 (brs, 1H), 2.73-2.69 (m, 1H), 2.70 (s, 6H), 2.52 (dd, 1H, J=15.0, 3.0 Hz), 2.07 (t, 1H, J=13.8 Hz), 1.28 (brs, 3H), 1.04 (brs, 3H); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₈H₃₉N₄O₇, 543.2813. Found, 543.2821.

Example 31 Synthesis of C5a-N,N′-Hydroxyethylmethylaminomethylminocycline 44

Anhydrous magnesium bromide (7.2 mg, 0.039 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (15.0 mg, 0.020 mmol, 1 equiv) and 2-(methylamino)ethanol (16 μL, 0.197 mmol, 10 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 55° C. After stirring at this temperature for 39 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (10 mL) and saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by flash-column chromatography (50% ethyl acetate-hexanes, grading to 100% ethyl acetate). The product of cyclopropane ring-opening was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 10½ h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.4 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1½ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 32-34 min were collected and concentrated, affording C5a-N,N′-hydroxyethylmethylaminomethylminocycline trifluoroacetate 44 as a yellow solid (3.7 mg, 29%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.52 (d, 1H, J=8.4 Hz), 6.94 (d, 1H, J=9.0 Hz), 3.85 (brs, 2H), 3.64 (d, 1H, J=16.8 Hz), 3.34-3.23 (m, 3H), 3.19-3.10 (m, 2H), 3.12 (s, 6H), 2.76 (brs, 3H), 2.65 (brs, 7H), 2.52 (dd, 1H, J=15.0, 2.4 Hz), 2.02-1.94 (m, 1H); HRMS-ESI (m/z): [M+H] calcd for C₂₇H₃₇N₄O₈, 545.2606. Found, 545.2609.

Example 32 Synthesis of C5a-(3-Dimethylaminopropyl)aminomethylminocycline 45

Anhydrous magnesium bromide (7.2 mg, 0.039 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (15.0 mg, 0.020 mmol, 1 equiv) and 3-dimethylamino-1-propylamine (25 μL, 0.197 mmol, 10 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 55° C. After stirring at this temperature for 17 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (10 mL) and saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the product of cyclopropane ring-opening was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 17 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate trihydrate (10.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.4 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 2¼ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→35% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 29-31 min were collected and concentrated, affording C5a-(3-dimethylaminopropyl)aminomethylminocycline trifluoroacetate 45 as a yellow solid (1.8 mg, 13%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.63 (d, 1H, J=9.0 Hz), 6.97 (d, 1H, J=9.6 Hz), 4.02 (d, 1H, J=2.4 Hz), 3.55 (d, 1H, J=16.8 Hz), 3.49 (d, 1H, J=14.4. Hz), 3.21-3.09 (m, 3H), 3.13 (s, 6H), 3.02-2.85 (m, 3H), 2.84 (s, 6H), 2.83 (s, 6H), 2.79 (d, 1H, J=16.8 Hz), 2.41 (dd, 1H, J=15.0, 3.0 Hz), 2.14-2.02 (m, 2H), 2.00 (t, 1H, J=13.8 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₉H₄₂N₅O₇, 572.3079. Found, 572.3081.

Example 33 Synthesis of C5a-Methoxyethoxymethylminocycline 46

Anhydrous magnesium bromide (6.2 mg, 0.034 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (13.0 mg, 0.017 mmol, 1 equiv) in 2-methoxyethanol (0.5 mL) at 23° C. The resulting solution was heated to 60° C. After stirring at 60° C. for 26 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 10 mL) and dichloromethane (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 10½ h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 2.8 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1% h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 32-34 min were collected and concentrated, affording C5a-methoxyethoxymethylminocycline trifluoroacetate 46 as a yellow solid (5.8 mg, 52%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.83 (d, 1 h, J=9.0 Hz), 7.05 (d, 1H, J=9.0 Hz), 4.13 (s, 1H), 3.54-3.45 (m, 4H), 3.44-3.40 (m, 1H), 3.34 (d, 1H, J=15.6 Hz), 3.27-3.25 (m, 1H), 3.26 (s, 3H), 3.18 (s, 6H), 3.11 (brd, 1H, J=14.4. Hz), 2.99 (s, 6H), 2.61 (d, 1H, J=16.2 Hz), 2.45 (dd, 1H, J=14.4, 3.0 Hz), 1.71 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₇H₃₆N₃O₉, 546.2446. Found, 546.2459.

Example 34 Synthesis of C5a-N-Imidazolylmethylminocycline 47

Anhydrous magnesium bromide (7.2 mg, 0.039 mmol, 3.0 equiv) was added to a solution of cyclopropane 22 (10.0 mg, 0.013 mmol, 1 equiv) and imidazole (6.2 mg, 0.091 mmol, 7.0 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 60° C. After stirring at this temperature for 60 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (15 mL) and saturated aqueous sodium bicarbonate solution (15 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (15 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue, the crude product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 18 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate (3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 3.6 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1¼ h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 25-27 min were collected and concentrated, affording C5a-imidazolylmethylminocycline trifluoroacetate 47 as a yellow solid (7.3 mg, 86%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 8.42 (t, 1H, J=1.2 Hz), 7.51 (d, 1H, J=9.0 Hz), 7.40 (t, 1H, J=1.8 Hz), 7.23 (t, 1H, J=1.8 Hz), 6.86 (d, 1H, J=9.0 Hz), 4.48 (AB quartet, 2H, J=14.4 Hz, Δν=44.4 Hz), 4.13 (s, 1H), 3.42 (d, 1H, J=16.8 Hz), 3.25 (dd, 1H, J=13.8, 1.2 Hz), 3.11 (s, 6H), 2.73 (s, 6H), 2.69 (d, 1H, J=16.2 Hz), 2.14 (dd, 1H, J=15.0, 3.0 Hz), 1.98 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₇H₃₂N₅O₇, 538.2296. Found, 538.2285.

Example 35 Synthesis of C5a-Pyridin-3-aminomethylminocycline 48

Anhydrous magnesium bromide (9.7 mg, 0.057 mmol, 2.0 equiv) was added to a solution of cyclopropane 22 (20.0 mg, 0.026 mmol, 1 equiv) and 3-aminopyridine (12.3 mg, 0.131 mmol, 5.0 equiv) in tetrahydrofuran (0.5 mL) at 23° C. The reaction flask was sealed and the mixture was heated to 60° C. After stirring at this temperature for 34 h, the reaction mixture was allowed to cool to 23° C. The cooled solution was partitioned between dichloromethane (15 mL) and saturated aqueous sodium bicarbonate solution (15 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (15 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: water, Solvent B: methanol, injection volume: 1.0 mL (methanol), gradient elution with 70→100% B over 50 min, flow rate: 15 mL/min]. Fractions eluting at 8-16 min were collected and concentrated. The orange residue, the product of cyclopropane ring-opening, was dissolved in acetonitrile (1.2 mL). The resulting solution was transferred to a polypropylene reaction vessel and concentrated aqueous hydrofluoric acid solution (48 wt %, 0.8 mL) was added. The reaction mixture was stirred vigorously at 23° C. for 24 h, then was poured into water (30 mL) containing dipotassium hydrogenphosphate (8.0 g). The resulting mixture was extracted with ethyl acetate-methanol (10:1, 3×40 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Palladium black (5.0 mg, 0.047 mmol, 1.8 equiv) was added in one portion to a solution of the crude product in methanol (1.0 mL) and dioxane (1.0 mL) at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 2 h, whereupon more palladium black (5.0 mg) was added. The resulting mixture was stirred at 23° C. for a further 2 h, then was filtered through a plug of Celite. The filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 26-28 min were collected and concentrated, affording C5a-pyridin-3-aminomethylminocycline trifluoroacetate 48 as a yellow solid (4.0 mg, 23%, three steps). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.58 (d, 1H, J=1.8 Hz), 7.56 (d, 1H, J=5.4 Hz), 7.42 (d, 1H, J=9.0 Hz), 7.34-7.28 (m, 2H), 6.67 (d, 1H, J=8.4 Hz), 4.82 (d, 1H, J=13.2 Hz), 4.61 (d, 1H, J=13.2 Hz), 4.15 (s, 1H), 3.71 (d, 1H, J=16.8 Hz), 3.24 (d, 1H, J=13.8 Hz), 3.08 (s, 6H), 2.80 (d, 1H, J=16.8 Hz), 2.75 (s, 6H), 2.24 (dd, 1H, J=14.4, 3.0 Hz), 2.09 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₉H₃₄N₅O₇, 564.2453; found 564.2457.

Example 36 Synthesis of C5a-Aminomethylminocycline 49

A solution of trimethylphosphine in tetrahydrofuran (1.0 M, 398 μL, 0.398 mmol, 2.0 equiv) was added dropwise via syringe to a solution of alkyl azide 23 (160 mg, 0.199 mmol, 1 equiv) and 2-(tert-butoxycarbonyloxyimino)-2-phenylacetonitrile (98.0 mg, 0.398 mmol, 2.0 equiv) in tetrahydrofuran at −10° C. The reaction mixture was allowed to warm to 23° C. over 15 min, then was stirred at this temperature for a further 15 h. The resulting solution was partitioned between dichloromethane (60 mL) and water (60 mL). The phases were separated and the organic phase was washed sequentially with water (60 mL) and saturated aqueous sodium chloride solution (2×60 mL). The organic solution was then dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by flash-column chromatography (25% ethyl acetate-hexanes), providing the corresponding tert-butoxycarbamate as a yellow solid (90 mg, 51%).

Methanol (2.5 mL) and dioxane (2.5 mL) were added to this product, forming a yellow solution. Palladium black (25 mg, 0.235 mmol, 2.3 equiv) was added in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23° C. for 1 h, whereupon more palladium black (25 mg) was added. The resulting mixture was stirred at 23° C. for a further 2 h, then was filtered through a plug of Celite. The filtrate was concentrated, providing an orange solid. Concentrated aqueous hydrofluoric acid (48 wt %, 1.4 mL) was added to a solution of the crude product in acetonitrile (2.0 mL) in a polypropylene reaction vessel at 23° C. The reaction mixture was stirred vigorously at 23° C. for 15 h. Excess hydrofluoric acid was quenched by the careful addition of methoxytrimethylsilane (9.0 mL). The resulting mixture was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 22-27 min were collected and concentrated, affording C5a-aminomethylminocycline trifluoroacetate 49 as a yellow solid (50 mg, 42%, three steps). ¹H NMR (500 MHz, CD₃OD, trifluoroacetate) δ 7.88 (d, 1H, J=9.0 Hz), 7.10 (d, 1H, J=9.0 Hz), 4.09 (d, 1H, J=2.5 Hz), 3.60 (d, 1H, J=17.0 Hz), 3.34 (d, 1H, J=14.5 Hz), 3.18 (s, 6H), 3.16 (s, 6H), 3.20-3.14 (m, 1H), 3.02 (d, 1H, J=14.5 Hz), 2.95 (d, 1H, J=17.0 Hz), 2.33 (dd, 1H, J=15.0, 3.0 Hz), 1.96 (t, 1H, J=14.5 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₄H₃₁N₄O₇, 487.2187. Found 487.2181.

Example 37 Synthesis of C5a-N-Acetylaminomethylminocycline 50

Acetyl chloride (0.9 μL, 0.013 mmol, 2.0 equiv) was added to a solution of C5a-aminomethylminocycline trifluoroacetate 49 (4.0 mg, 0.0067 mmol, 1 equiv) and N,N-diisopropylethylamine (4.6 μL, 0.027 mmol, 4.0 equiv) in methanol (200 μL) at 0° C. The resulting solution was allowed to warm to 23° C. over 5 min. The reaction mixture was stirred at this temperature for 1 h, then was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 25-28 min were collected and concentrated, affording C5a-N-acetylaminomethylminocycline trifluoroacetate 50 as a yellow solid (3.2 mg, 75%). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) S 7.80 (d, 1H, J=9.0 Hz), 7.03 (d, 1H, J=9.0 Hz), 3.89 (s, 1H), 3.46 (d, 1H, J=14.4 Hz), 3.27 (d, 1H, J=13.8 Hz), 3.23 (d, 1H, J=16.8 Hz), 3.15-3.08 (m, 13H), 2.63 (d, 1H, J=16.2 Hz), 2.11 (dd, 1H, J=14.4, 2.4 Hz), 1.91 (s, 3H), 1.69 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₆H₃₃N₄O₈, 529.2293. Found 529.2299.

Example 38 Synthesis of C5a-N-Trimethylacetylaminomethylminocycline 51

Trimethylacetyl chloride (1.6 μL, 0.013 mmol, 2.0 equiv) was added to a solution of C5a-aminomethylminocycline trifluoroacetate 49 (4.0 mg, 0.0067 mmol, 1 equiv) and N,N-diisopropylethylamine (4.6 μL, 0.027 mmol, 4.0 equiv) in methanol (200 μL) at 23° C. The reaction mixture was stirred at this temperature for 1½ h, then was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 38-40 min were collected and concentrated, affording C5a-N-trimethylacetylaminomethylminocycline trifluoroacetate 51 as a yellow solid (3.0 mg, 66%). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.73 (d, 1H, J=9.0 Hz), 6.99 (d, 1H, J=9.6 Hz), 3.92 (s, 1H), 3.54 (d, 1H, J=14.4 Hz), 3.30-3.25 (m, 2H), 3.11 (s, 6H), 3.06-3.00 (m, 1H), 3.03 (s, 6H), 2.59 (d, 1H, J=16.2 Hz), 2.03 (dd, 1H, J=14.4, 3.0 Hz), 1.71 (t, 1H, J=14.4 Hz), 1.11 (s, 9H); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₉H₃₉N₄O₈, 571.2762. Found 571.2771.

Example 39 Synthesis of C5a-N-Benzoylaminomethylminocycline 52

Benzoyl chloride (1.5 μL, 0.013 mmol, 2.0 equiv) was added to a solution of C5a-aminomethylminocycline trifluoroacetate 49 (4.0 mg, 0.0067 mmol, 1 equiv) and N,N-diisopropylethylamine (4.6 μL, 0.027 mmol, 4.0 equiv) in methanol (200 μL) at 23° C. The reaction mixture was stirred at this temperature for 1½ h, then was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 38-40 min were collected and concentrated, affording C5a-N-benzoylaminomethylminocycline trifluoroacetate 52 as a yellow solid (1.6 mg, 34%). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.75 (d, 2H, J=7.2 Hz), 7.70 (d, 1H, J=9.6 Hz), 7.54 (t, 1H, J=7.8 Hz), 7.45 (t, 2H, J=7.8 Hz), 6.95 (d, 1H, J=9.0 Hz), 3.94 (s, 1H), 3.74 (d, 1H, J=14.4 Hz), 3.37 (d, 1H, J=15.6 Hz), 3.36-3.27 (m, 2H), 3.13 (s, 6H), 3.02 (s, 6H), 2.63 (d, 1H, J=16.2 Hz), 2.21 (dd, 1H, J=14.4, 2.4 Hz), 1.76 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₃₁H₃₅N₄O₈, 591.2449. Found 591.2459.

Example 40 Synthesis of C5a-N-Methoxyacetylaminomethylminocycline 53

Methoxyacetyl chloride (1.2 μL, 0.013 mmol, 2.0 equiv) was added to a solution of C5a-aminomethylminocycline trifluoroacetate 49 (4.0 mg, 0.0067 mmol, 1 equiv) and N,N-diisopropylethylamine (4.6 μL, 0.027 mmol, 4.0 equiv) in methanol (200 μL) at 23° C. The reaction mixture was stirred at this temperature for 2 h, then was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 28-30 min were collected and concentrated, affording C5a-N-methoxyacetylaminomethylminocycline trifluoroacetate 53 as a yellow solid (2.0 mg, 45%). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.75 (d, 1H, J=9.0 Hz), 7.00 (d, 1H, J=9.0 Hz), 3.92 (s, 1H), 3.84 (AB quartet, 2H, J=15.0 Hz, Δν=10.2 Hz), 3.59 (d, 1H, J=14.4 Hz), 3.40 (s, 3H), 3.32-3.28 (m, 1H), 3.27 (d, 1H, J=15.6 Hz), 3.10 (s, 6H), 3.10-3.07 (m, 1H), 3.03 (s, 6H), 2.58 (d, 1H, J=16.2 Hz), 2.09 (dd, 1H, J=14.4, 3.0 Hz), 1.69 (t, 1H, J=13.8 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₇H₃₄N₄O₉, 559.2399. Found 559.2435.

Example 41 Synthesis of C5a-N-3,5-Difluorobenzoylaminomethylminocycline 54

3,5-Difluorobenzoyl chloride (1.9 μL, 0.013 mmol, 2.0 equiv) was added to a solution of C5a-aminomethylminocycline trifluoroacetate 49 (4.0 mg, 0.0067 mmol, 1 equiv) and N,N-diisopropylethylamine (4.6 μL, 0.027 mmol, 4.0 equiv) in methanol (200 μL) at 23° C. The reaction mixture was stirred at this temperature for 2 h, then was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 43-45 min were collected and concentrated, affording C5a-N-3,5-difluorobenzoylaminomethylminocycline trifluoroacetate 54 as a yellow solid (1.5 mg, 30%). ¹H NMR (600 MHz, CD₃OD, trifluoroacetate) δ 7.70 (d, 1H, J=9.0 Hz), 7.37-7.34 (m, 2H), 7.19-7.14 (m, 1H), 6.95 (d, 1H, J=9.0 Hz), 3.95 (s, 1H), 3.74 (d, 1H, J=14.4 Hz), 3.40-3.33 (m, 2H), 3.26 (d, 1H, J=13.8 Hz), 3.13 (s, 6H), 3.01 (s, 6H), 2.62 (d, 1H, J=16.2 Hz), 2.20 (dd, 1H, J=13.8, 2.4 Hz), 1.75 (t, 1H, J=13.8 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₃₁H₃₃F₂N₄O₈, 627.2261. Found 627.2123.

Example 42 Synthesis of C5a-N-Methanesulfonylaminomethylminocycline 55

Methanesulfonic anhydride (2.3 mg, 0.013 mmol, 2.0 equiv) was added to a solution of C5a-aminomethylminocycline trifluoroacetate 49 (4.0 mg, 0.0067 mmol, 1 equiv) and N,N-diisopropylethylamine (4.6 μl, 0.027 mmol, 4.0 equiv) in methanol (200 μL) at 23° C. The reaction mixture was stirred at this temperature for 2 h, then was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C18 column [10 μm, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, injection volume: 5.0 mL (4.0 mL 0.1% trifluoroacetic acid in water, 1.0 mL acetonitrile), gradient elution with 5→40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 28-30 min were collected and concentrated, affording C5a N-methanesulfonylaminomethylminocycline trifluoroacetate 55 as a yellow solid (1.5 mg, 33%).

¹H NMR (600 MHz, CD₃OD, trifluoroacetate) S 7.77 (d, 1H, J=9.0 Hz), 7.01 (d, 1H, J=9.0 Hz), 3.91 (s, 1H), 3.34 (d, 1H, J=16.2 Hz), 3.26-3.21 (m, 2H), 3.08 (s, 6H), 3.03 (s, 6H), 2.99 (d, 1H, J=13.8 Hz), 2.86 (s, 3H), 2.60 (d, 1H, J=16.2 Hz), 2.35 (dd, 1H, J=14.4, 3.0 Hz), 1.70 (t, 1H, J=14.4 Hz); HRMS-ESI (m/z): [M+H]⁺ calcd for C₂₅H₃₂N₄O₉S, 565.1963; found 565.1973.

Example 43 Preparation of β-Methylenone 59 from Enone 56

Step 1. Synthesis of β-Phenylthio Ketone 57

To a solution of enone 56 (1.94 g, 4.03 mmol, 1 equiv) in dichloromethane (9 mL) was added triethylamine (56 μL, 0.40 mmol, 0.1 equiv). The solution was cooled to 0° C. then thiophenol (434 μL, 4.23 mmol, 1.05 equiv) was added dropwise and the reaction was stirred at 0° C. After forty minutes, additional thiophenol was added (40 μL, 0.39 mmol, 0.1 equiv). Seven minutes later, acetic acid (26 μL, 0.40 mmol, 0.1 equiv) was added, and the reaction was concentrated under reduced pressure to remove the solvent. Purification of the resulting crude oil via flash column chromatography on silica gel (Biotage, 100 g, 5 to 30% EtOAc in hexane gradient) provided enone 57 as a white foam (2.33 g, 97%, 6:1 mixture of diastereomers): ¹H NMR (400 MHz, CDCl₃; mixture of diastereomers, 6:1 H:H′) δ 7.43-7.37 (m, 2H+2H′), 7.36-7.19 (m, 8H, 8H′), 5.29 (s, 2H), 5.26 (s, 2H′), 4.31 (d, J=9.2 Hz, 1H), 3.84-3.73 (m, 1H), 3.63 (d, J=11.6 Hz, 1H′), 3.42-3.31 (m, 1H′), 3.25 (dd, J=6.7, 14.0, 1 H), 3.12 (t, J=12.8 Hz, 1H′), 2.63-2.47 (m, 2H+2H′), 2.40 (s, 6H), 2.38 (s, 6H′), 2.33-2.21 (m, 2H+2H′), 0.81 (s, 9H′), 0.79 (s, 9H), 0.050 (s, 3H′), 0.037 (s, 3H), 0.02 (s, 3H′), 0.00 (s, 3H); MS (ESI) m/z 591.31 (M−H).

Step 2. Synthesis of β-Phenylthio Enone 58

To a solution of enone 57 (2.34 g, 3.94 mmol, 1 equiv) in dichloromethane (12 mL) at 0° C. was added pyridine (476 μL, 5.91 mmol, 1.5 equiv) followed by N-chlorosuccinimide (NCS, 634 mg, 4.75 mmol, 1.2 equiv). The solution was allowed to warm to ambient temperature, during which the NCS dissolved into solution. After 2 h, additional NCS (1.2 equiv, as above) and pyridine (1.5 equiv, as above) were added at ambient temperature. After an additional 3.5 h, the resulting brown solution was poured into aqueous NaOH solution (1 N, 15 mL) and extracted with EtOAc (3×60 mL). The combined organic layers were washed with aqueous NaOH solution (1 N, 10 mL), water (20 mL), and brine (20 mL) then dried (Na₂SO₄), filtered, and concentrated under reduced pressure. Purification of the resulting oil via flash column chromatography on silica gel (Biotage, 100 g, 5 to 40% EtOAc in hexane gradient) provided enone 58 as a yellow foam (1.89 g, 81%): ¹H NMR (400 MHz, CDCl₃) δ 7.50-7.39 (m, 7H), 7.38-7.28 (m, 3H), 5.44 (d, J=2.4 Hz, 1H), 5.31 (dd, J=12.2, 15.3 Hz, 2H), 3.80 (d, J=11.0 Hz, 1H), 3.10 (ddd, J=2.44, 4.27, 18.3 Hz, 1H), 2.98 (d, J=1.2 Hz, 18.3 Hz, 1H), 2.73 (ddd, J=1.8, 4.9, 10.4 Hz, 1H), 2.47 (s, 6H), 0.86 (s, 9H), 0.24 (s, 3H), 0.00 (s, 3H); MS (ESI) m/z 589.29 (M−H).

Step 3. Synthesis of β-Methyl Enone 59

A flame-dried flask was cooled under nitrogen atmosphere and charged with copper iodide (CuI, 242 mg, 1.27 mmol, 1.15 equiv). The flask was evacuated and back-filled with nitrogen three times, then Et₂O (10 mL) was added. The resulting gray suspension was cooled to −78° C. and methyllithium (1.6 M in Et₂O; 1.51 mL, 2.2 equiv) was added dropwise. After 5 min the solution was removed from the bath and swirled until the solution was homogeneous (5 min, a slight yellow color was also observed). The solution was recooled to −78° C. for 10 min. Vacuum-dried enone 58 (650 mg, 1.10 mmol, 1 equiv) in Et₂O (5 mL) under nitrogen was added dropwise via syringe to the cold cuprate solution over 5 min. An orange color develops during the addition, followed by the appearance of an orange-yellow precipitate. After 30 min, excess cuprate was quenched via the addition of saturated aqueous ammonium chloride (3 mL) and warming to ambient temperature. The solution was poured into saturated aqueous ammonium chloride (20 mL) and water (15 mL) and extracted with EtOAc (3×60 mL). The combined organic layers were washed sequentially with water (30 mL) and brine (10 mL), dried (Na₂SO₄), filtered, and concentrated under reduced pressure. Purification of the resulting oil via flash column chromatography on silica gel (Biotage, 100 g, 5 to 40% EtOAc in hexane gradient) provided enone 59 as a yellow solid (387 mg, 71%): ¹H NMR (400 MHz, CDCl₃) δ 7.45 (d, J=7.9 Hz, 2H), 7.38-7.26 (m, 3H), 5.89 (s, 1H), 5.31 (s, 2H), 3.68 (d, J=20.1 Hz, 1H), 2.80-2.61 (m, 3H), 2.41 (s, 6H), 1.96 (s, 3H), 0.77 (s, 9H), 0.21 (s, 3H), 0.00 (s, 3H); MS (ESI) m/z 495.33 (M−H).

Example 44 Preparation of Phenyl 2-(benzyloxy)-3-(dibenzylamino)-5-fluoro-6-methylbenzoate 67 from 5-Fluoro-2-methoxybenzoic acid 60

Step 1. Synthesis of 3-fluoro-6-methoxy-2-methylbenzoic acid 61

Diisopropyl amine (478 g, 4.725 mol) and anhydrous THF (2.8 L) were charged to a 10 L 4-neck flask equipped with gas inlet, addition funnel, thermometer and mechanical stirrer. The solution was degassed with N₂ for 5 min then cooled to −78° C. with dry ice acetone bath under N₂ flow. A solution of n-BuLi in n-hexane (1.8 L, 2.5 M, 4.5 mol) was added to the stirring mixture at −20° C.-10° C. over 40 min. After the addition, the reaction was stirred at −20° C. for 40 min. A solution of 5-fluoro-2-methoxybenzoic acid 60 (297.5 g, 1.75 mol) in anhydrous THF (1.3 L) was added to the reaction mixture at −55° C.—45° C. with stirring over 60 min. The resulting brown mixture was stirred at −15˜−25° C. for 3.5 h. The reaction mixture turned to red brown. Another para-reaction same with above reaction was set at same time. A 20 L four-neck flask equipped with gas inlet, addition funnel, thermometer and mechanical stirrer was charged with neat MeI (1500 g, 10.5 mol) and anhydrous THF (2.6 L). The mixture was degassed with N₂ for 5 min and cooled to −20˜−15° C. with dry ice acetone bath under small N₂ flow. The obtained solution from the above two para-reactions was transferred to the 20 L flask containing MeI at −15˜−5° C. with stirring over 20 min. The resulting cloudy mixture was stirred at −20˜−15° C. for 2 h and brought to ambient temperature over 1.5 h. The obtained brown suspension was stirred at 25˜30° C. for 16 h. The reaction was then quenched with aqueous HCl (5.0 L, 2N) at 20˜25° C. and diluted MTBE (3.0 L). After being stirred for 5 min at 20° C., the two phase mixture was separated, and the upper layer was concentrated to dryness under vacuum to give black oil. The aqueous layer was extracted with EtOAc (5×1.5 L) and all the organic layers were combined with the black oil. The resulting solution was washed with water (2×μL) and brine (3×1 L). The organic layer was dried over Na₂SO₄ and filtered. The filtrate was concentrated under reduce pressure to afford crude 3-fluoro-6-methoxy-2-methylbenzoic acid 61 (740 g, >100%) as brown crystal solid that was used in the next step without further purification: ¹H NMR (400 MHz, CDCl₃) δ 7.06 (dd, J=9.8, 8.5 Hz, 1H), 6.75 (dd, J=9.8, 3.7 Hz, 1H), 3.86 (s, 3H), 2.34 (d, J=2.4 Hz, 3H); MS (ESI) m/z 185.12 (M+H).

Step 2. Synthesis of Phenyl 3-fluoro-6-methoxy-2-methylbenzoate 62

A 20 L 3-neck flask, equipped with mechanical stirrer, addition funnel and thermometer was charged with a solution of compound 61 (740 g, 4.02 mol) in anhydrous CH₂Cl₂(8.0 L) followed by several drops of DMF. The solution was degassed with N₂ for 3 min. (COCl)₂ (880 g, 6.93 mol) was added to the stirring reaction mixture slowly and carefully at 25-27° C. over 45 min. A lot of gas was generated. After stirring at 25-27° C. for 60 min, the reaction mixture was concentrated to dryness under reduced pressure. The residual oil was re-dissolved in anhydrous CH₂Cl₂ (2.0 L), concentrated to dryness again and further dried with under reduced pressure for 40 min to give black oil that was dissolved in anhydrous CH₂Cl₂(8.0 L). PhOH (460 g, 4.9 mol) was added to the stirred solution at 25-30° C., followed by Et₃N (824 g, 8.16 mol). After DMAP (4.9 g, 0.04 mol) was added to the reaction, the reaction mixture was stirred at 20-30° C. for 16 h. Aqueous HCl (2.0 L, 3N) was added to the reaction mixture below 30° C. The organic layer was separated and washed with 3N aqueous HCl (2×1 L). The organic layer was concentrated to dryness under reduce pressure to give brown oil that was dissolved in EtOAc (4.0 L) and washed with 0.5N aqueous (3×1.0 L) and brine (2×1.0 L). The above acid aqueous layer was extracted with EtOAc (2×1.0 L) and the extracts were combined with the above EtOAc solution. The organic layer was dried over Na₂SO₄ and filtered. The filtrate was concentrated under reduce pressure to afford crude compound 62 (1100 g) as brown partially crystalline slurry (>100% yield): ¹H NMR (400 MHz, CDCl₃) δ 7.47-7.41 (m, 2H), 7.31-7.24 (m, 3H), 7.08 (dd, J=9.2, 9.2 Hz, 1H), 6.77 (dd, J=9.2, 3.7 Hz, 1H), 3.88 (s, 3H), 2.36 (d, J=2.3 Hz, 3H); MS (ESI) m/z 261.12 (M+H).

Step 3. Synthesis of Phenyl 3-fluoro-6-hydroxy-2-methylbenzoate 63

A 30 L 4-neck flask equipped with mechanical stirrer, thermometer and gas inlet was charged with a solution of compound 62 (1140 g, 4.38 mol) in CH₂Cl₂ (15 L). The brown solution was cooled to −78° C. with dry ice acetone bath under small N₂ flow. A solution of BBr₃ in CH₂Cl₂ (4.5 L, 5.26 mol) was added to the reaction at −70˜−78° C. with stirring over 74 min. The reaction mixture was the allowed to warm to 20˜25° C. over 3 h and stirred at room temperature for 16 h. Saturated aqueous NaHCO₃ was added to the reaction mixture slowly to pH 2˜3. After stirring for 5 min, the layers were separated and the aqueous layer was extracted with CH₂Cl₂ (2×1 L). The organic layers were combined and washed with brine (2×2 L). The organic layer was dried over Na₂SO₄ and filtered and the filtrate was concentrated under reduced pressure to give 1100 g (>100%) of crude compound 63 as brown oil: ¹H NMR (400 MHz, CDCl₃) δ 10.66 (s, 1H), 7.50-7.44 (m, 2H), 7.36-7.31 (m, 1 H), 7.26-7.18 (m, 3H), 6.86 (dd, J=9.3, 4.9 Hz, 1H), 2.60 (d, J=2.4 Hz, 3H); MS (ESI) m/z 245.11 (M−H).

Step 4. Synthesis of phenyl 3-fluoro-6-hydroxy-2-methyl-5-nitrobenzoate 64

A 30 L 4-neck flask equipped with mechanical stirrer, thermometer and addition funnel was charged with a solution of compound 63 (1100 g, 4.47 mol) in CH₂Cl₂ (8.0 L) followed by water (8.1 L) and tetrabutyl ammonium bromide (144 g, 0.45 mol). Aqueous HNO₃ (591 mL, 68 w %, 8.94 mol) was added to the stirred two-phase reaction mixture at 24˜27° C. over 3 min and the mixture was stirred at 24˜28° C. for 20 h. The two layers were separated and the aqueous layer was extracted with CH₂Cl₂ (4×1.0 L). The organic layers were then combined and successively washed with water (3×1.0 L) and brine (2×2 L). The organic layer was dried over Na₂SO₄ and filtered and concentrated under reduce pressure to give 1423 g (>100%) of compound 64 as dark brown solid.

Step 5. Synthesis of phenyl 2-(benzyloxy)-5-fluoro-6-methyl-3-nitrobenzoate 65

A 30 L 4-neck flask equipped with mechanical stirrer, thermometer, addition funnel and gas inlet was charged with a solution of compound 64 (1423 g, 4.89 mol) in acetone (17 L). K₂CO₃ (1350 g, 9.8 mol) and KI (81 g, 0.49 mol) were added to the stirring reaction mixture and the resulting suspension was degassed with N₂ for 5 min prior to adding BnBr (878.2 g, 5.13 mol) at 27˜29° C. over 8 min. After the addition, the brown suspension was refluxed for 2.5 h, then allowed to cool to 20˜30° C. The suspension was filtered, and the filter cake was washed with acetone (3×900 mL). The filtrate was concentrated under reduced pressure and the residual oil was dissolved in MTBE (7.0 L) and successively washed with water (5×1.0 L) and brine (4×1.0 L). The organic layer was dried over Na₂SO₄ filtered then concentrated to dryness under reduced pressure to afford 1840 g of crude compound 65 (98.7% yield) as brown oil.

Step 6. Synthesis of Phenyl 3-amino-2-(benzyloxy)-5-fluoro-6-methylbenzoate 66

A solution of compound 65 (700 g, 1.84 mol) in THF (7 L) was cooled to 12° C. and stirred while adding a solution of Na₂S₂O₄ (1599 g, 9.18 mol) in water (7.0 L) was added to the reaction with stirring. The exotherm was controlled by addition rate so that the reaction mixture temperature was below 17° C. The reaction mixture was then allowed to stir for 15 hours prior to adding 15.3 L EtOAc. The layers were separated and the organic layer was washed with successively with water (2×4 L and brine (1×4 L). The organic was dried over Na₂SO₄ and concentrated to give 699 g of a brownish solid that was recrystallized from heptane/toluene to afford 532 g (82.7%) of desired compound 66 obtained as an off-white solid.

Step 7. Synthesis of Phenyl 2-(benzyloxy)-3-(dibenzylamino)-5-fluoro-6-methylbenzoate 67

To a solution of 500 g of compound 66 in 4.25 L N-methylpyrrolidinone was added N,N-diisopropylethylamine (620 ml) followed by BnBr (425 mL, 2.5 equiv.). The mixture was heated at 100° C. for 18 h then cooled to 8° C. and treated over 10 min with 25% w/w aqueous triethyl amine aqueous. The mixture was allowed to stir for 25 minutes at ambient temperature before being cooled to 15° C. adding water (10 L) over ca. 3 hours to precipitate product. The obtained pale colored suspension was filtered then washed with 2 L water and dried. The crude product (750 g) was then dissolved in 4.1 L toluene and filtered through silica gel to give 762 g of a yellow solid that was recrystallized from acetone/heptane to afford 606 g of desired compound 67 (80% yield) obtained as an off-white solid: ¹H NMR (400 MHz, CDCl₃) δ 7.48-7.03 (m, 20H), 6.60 (d, J=11.5 Hz, 1H), 5.31 (s, 2H), 4.33 (s, 4H), 2.30 (s, 3H).

Example 45 Preparation of 5a-Methyl-7-amido tetracyclines 70 from Phenyl 2-(benzyloxy)-3-(dibenzylamino)-5-fluoro-6-methylbenzoate 67

Step 1. Synthesis of 7-Fluoro-9-dibenzyl analog 68

To a solution of lithium diisopropylamide (2.0 M in hexanes, 478 μL, 0.959 mmol, 2 equiv) and TMEDA (144 μL, 0.957 mmol, 2 equiv) in THF (8 mL) at −78° C. was added a solution of compound 67 (509 mg, 0.957 mmol, 2 equiv) in THF (2 mL) by dropwise addition. This resulted in a dark red colored solution. After 10 min, a solution of enone 59 (235 mg, 0.473 mmol, 1 equiv) in THF (1 mL) was added, followed by slow addition of LHMDS (1 M in hexanes; 957 μL, 0.957 mmol, 2 equiv). The reaction mixture was allowed to warm to −15° C. over 80 min. Excess base was quenched by the addition of a saturated, aqueous solution of ammonium chloride (1 mL). The solution was warmed to ambient temperature, poured into a saturated, aqueous solution of ammonium chloride (15 mL) and water (5 mL) and extracted with EtOAc (2×25 mL). The combined organic extracts were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. Purification of the resulting oil via flash column chromatography on silica gel (Silicycle, 40 g, 5 to 12.5% EtOAc in hexanes gradient) provided 7-fluoro-9-dibenzyl analog 68 as a yellow oil (275 mg, 62%): ¹H NMR (400 MHz, CDCl₃) δ 16.59 (s, 1H), 7.53-7.44 (m, 4H), 7.41-7.20 (m, 12H), 7.18-7.10 (m, 4H), 6.65 (d, J=10.4 Hz, 1H), 5.38 (d, J=9.8 Hz, 1H), 5.36 (s, 2H), 5.07 (d, J=9.8 Hz, 1H), 4.36 (d, J=14.0 Hz, 2H), 4.21 (d, J=14.0 Hz, 2H), 4.04 (d, J=9.8 Hz, 1H), 2.89 (d, J=15.9 Hz, 1H), 2.66 (d, J=15.0 Hz, 1H), 2.48 (s, 6H), 2.32-2.22 (m, 1 H), 2.15 (dd, J=4.9, 12.7 Hz, 1H), 1.08 (s, 9H), 0.25 (s, 3H), 0.18 (s, 3H); MS (ESI) m/z 934.40 (M+H).

Step 2. Synthesis of 7-Fluoro-9-amino analog 69

To a solution of 68 (275 mg, 0.294 mmol, 1 equiv) in dioxane (1 mL) was added an aqueous solution of HF (50%, 350 μL). After 75 min, the reaction mixture was poured into an aqueous K₂HPO₄ solution (4.4 g in 35 mL) and extracted with EtOAc (2×30 mL). The combined organic layers were dried (Na₂SO₄), filtered, and concentrated under reduced pressure. Palladium on carbon (10%; 168 mg) was added to a solution of this crude oil in dioxane:MeOH (1:1, 6 mL). The flask was fitted with a septum and evacuated and back-filled three times with hydrogen gas. The reaction was stirred under an atmosphere (balloon) of hydrogen gas for 1 h. The reaction mixture was filtered through celite to remove the palladium catalyst and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil provided 115 mg of the desired compound 69 (73%): ¹H NMR (400 MHz, CD₃OD) δ 7.40 (d, J=9.2 Hz, 1H), 4.11 (s, 1H), 3.10-2.94 (m, 8H), 2.62 (d, J=15.9 Hz, 1H), 2.04 (dd, J=3.1, 14.0 Hz, 1H), 1.97-1.87 (m, 1H), 1.28 (s, 3H); MS (ESI) m/z 462.09 (M+H).

Step 3. Synthesis of 7-Fluoro-9-amido analog 70

Protocols for synthesizing various 7-fluoro-9-amido analogs are described in Examples 46-51.

Example 46 Synthesis of 7-Fluoro-9-amido analog 71

To an orange solution of aniline 69 (10.6 mg, 0.021 mmol, 1 equiv) in DMPU:CH₃CN (3:1, 400 μL) was added 2-(pyrrolidin-1-yl)acetyl chloride hydrochloride (5.2 mg, 0.028 mmol, 1.3 equiv). The solution lightens to yellow. After 45 min, the solvent was removed under reduced pressure. Removal of excess DMPU was achieved by precipitation of the desired salt via addition of HCl in MeOH (0.5 M, 200 μL) followed by Et₂O (5 mL). The precipitate was filtered off on celite with Et₂O wash, then rinsed off with MeOH and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil afforded 4.55 mg of the desired compound 71 (33%): ¹H NMR (400 MHz, CD₃OD) δ 8.25 (d, J=11.0 Hz, 1H), 4.33 (s, 2H), 4.10 (s, 1H), 3.84-3.73 (m, 2H), 3.26-3.14 (m, 2H), 3.08-2.95 (m, 8H), 2.55 (d, J=15.9 Hz, 1H), 2.25-1.97 (m, 5H), 1.96-1.84 (m, 1H), 1.26 (s, 3H); MS (ESI) m/z 573.13 (M+H).

Example 47 Synthesis of 7-Fluoro-9-amido analog 72

To an orange solution of 69 (11.7 mg, 0.023 mmol, 1 equiv) in DMPU:CH₃CN (3:1, 400 μL) was added 2-(tert-butylamino)acetyl chloride hydrochloride (7.3 mg, 0.039 mmol, 1.7 equiv). The solution lightens to yellow. After 1 h, the solvent was removed under reduced pressure. Removal of excess DMPU was achieved by precipitation of the desired salt via addition of HCl in MeOH (0.5 M, 200 μL) followed by Et₂O (3.5 mL). The precipitate was filtered off on celite with Et₂O wash, then rinsed off with MeOH and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil afforded 8.68 mg of the desired compound 72 (58%): ¹H NMR (400 MHz, CD₃OD) δ 8.27 (d, J=11.0 Hz, 1H), 4.14-4.06 (m, 3H), 3.10-2.96 (m, 8H), 2.55 (d, J=15.9 Hz, 1H), 2.03 (dd, J=2.4, 14.0 Hz, 1H), 1.95-1.85 (m, 1H), 1.42 (s, 9H), 1.27 (s, 3H); MS (ESI) m/z 575.14 (M+H).

Example 48 Synthesis of 7-Fluoro-9-amido analog 73

To a solution of compound 69 (10.0 mg, 0.020 mmol, 1 equiv) in DMPU:CH₃CN (3:1, 400 μL) was added 2-(dimethylamino)acetyl chloride hydrochloride (5.6 mg, 0.030 mmol, 1.5 equiv). The solution lightens to yellow. After 1.5 h, another 1.5 equiv of the acetyl chloride was added. After 3 h, the solvent was removed under reduced pressure. Removal of excess DMPU was achieved by precipitation of the desired salt via addition of HCl in MeOH (0.5 M, 200 μL) followed by Et₂O (3.5 mL). The precipitate was filtered off on Celite with Et₂O wash, then rinsed off with MeOH and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil afforded 5.58 mg of the desired compound 73 (45%): ¹H NMR (400 MHz, CD₃OD) δ 8.25 (d, J=11.0 Hz, 1H), 4.23 (s, 2H), 4.10 (s, 1H), 3.09-2.94 (m, 14H), 2.56 (d, 15.9 Hz, 1H), 2.04-1.98 (m, 1H), 1.95-1.85 (m, 1H), 1.26 (s, 3H); MS (ESI) m/z 547.16 (M+H).

Example 49 Synthesis of 7-Fluoro-9-amido analog 74

To a solution of 69 (11.8 g, 0.024 mmol, 1 equiv) in DMPU:CH₃CN (3:1, 400 μL) was added sodium carbonate (9.6 mg, 0.091 mmol, 3.8 equiv). After seven minutes bromoacetylbromide (2.3 μL, 0.026 mmol, 1.1 equiv) was added. The color lightens to yellow. After 45 min, N-ethylmethylamine (9.5 μL, 0.11 mmol, 4.5 equiv) was added. After an additional 19 h, the sodium carbonate was removed by celite filtration, followed by concentration under reduced pressure to remove excess amine. Removal of excess DMPU was achieved by precipitation of the desired salt via addition of HCl in MeOH (0.5 M, 200 μL) followed by Et₂O (8 mL). The precipitate was filtered off on celite with Et₂O wash, then rinsed off with MeOH and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil afforded 7.89 mg of the desired compound 74 (53%): ¹H NMR (400 MHz, CD₃OD) δ 8.25 (d, J=11.0 Hz, 1H), 4.30 (d, J=15.9 Hz, 1H), 4.18 (d, J=16.4 Hz, 1H), 4.10 (s, 1H), 3.43-3.21 (m, 2H), 3.09-2.95 (m, 11H), 2.56 (d, J=15.9 Hz, 1H), 2.05-1.99 (m, 1H), 1.95-1.86 (m, 1H), 1.38 (t, J=7.3 Hz, 3H), 1.26 (s, 3H); MS (ESI) m/z 561.13 (M+H).

Example 50 Synthesis of 7-Fluoro-9-amido analog 75

To a solution of compound 69 (10.1 g, 0.020 mmol, 1 equiv) in DMPU:CH₃CN (3:1, 400 μL) was added sodium carbonate (10.5 mg, 0.099 mmol, 5 equiv). After 15 min bromoacetylbromide (2.0 μL, 0.022 mmol, 1.1 equiv) was added. The color lightens to yellow. After 45 min, cyclopentylamine (9.4 μL, 0.095 mmol, 4.8 equiv) was added. After an additional 19 h, the sodium carbonate was removed by celite filtration, followed by concentration under reduced pressure to remove excess amine. Removal of excess DMPU was achieved by precipitation of the desired salt via addition of HCl in MeOH (0.5 M, 200 μL) followed by Et₂O (8 mL). The precipitate was filtered off on celite with Et₂O wash, then rinsed off with MeOH and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil provided 1.07 mg of the desired compound 75 (8%; 3.64 mg impure, 28%): ¹H NMR (400 MHz, CD₃OD) δ 8.26 (d. J=11.0 Hz, 1H), 4.09 (s, 3 H), 3.69-3.56 (m, 1H), 3.08-2.95 (m, 8H), 2.56 (d, J=15.9 Hz, 1H), 2.21-2.09 (m, 2H), 2.04-1.97 (m, 1H), 1.95-1.78 (m, 3H), 1.76-1.63 (m, 4H), 1.26 (s, 3H); MS (ESI) m/z 587.16 (M+H).

Example 51 Synthesis of 7-Fluoro-9-amido analog 76

To a suspension of methylated N-methylproline hydrochloride (34.6 mg, 0.21 mmol, 5 equiv) in NMP (500 μL) at 0° C. was added 1-propanephosphonic acid cyclic anhydride (150 μL, 0.25 mmol, 6 equiv). The solution was warmed to ambient temperature over twenty minutes, then compound 69 (21.1 mg, 0.042 mmol, 1 equiv) was added. The solution turned dark orange. After 55 min, removal of excess NMP was achieved by precipitation of the desired salt via addition of HCl in MeOH (0.5 M, 250 μL) followed by Et₂O (10 mL). The precipitate was filtered off on celite with Et₂O wash, then rinsed off with MeOH and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil provided 9.01 mg of the desired compound 76 (33%): ¹H NMR (400 MHz, CD₃OD) δ 8.19 (d, J=11.0 Hz, 1H), 4.37 (t, J=7.9 Hz, 1H), 4.10 (s, 1H), 3.82-3.73 (m, 1 H), 3.09-2.95 (m, 11H), 2.77-2.66 (m, 1H), 2.57 (d, J=15.9 Hz, 1H), 2.31-1.98 (m, 5H), 1.96-1.85 (m, 1H), 1.27 (s. 3H); MS (ESI) m/z 573.08 (M+H).

Example 52 Preparation of phenyl 4-(benzyloxy)-2-tert-butyl-7-fluoro-6-methylisoindoline-5-carboxylate 83 from Phenyl 3-fluoro-6-hydroxy-2-methylbenzoate 63

Step 1. Synthesis of Phenyl 3-bromo-5-fluoro-2-hydroxy-6-methylbenzoate 77 from Phenyl 3-fluoro-6-hydroxy-2-methylbenzoate 63

Compound 63 (4.92 g, 95% purity, 20 mmol) was dissolved in acetic acid (50 mL) and bromine (1.54 mL, 30 mmol) was added via syringe at room temp. After stirred at room temp for 2 hour, LC/MS indicated that the starting material was consumed. This reaction mixture was diluted with ethyl acetate, washed with water (3×100 mL) and brine. The organics were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. This gave 7.06 g of compound 77 as light yellow solid: ¹H NMR (400 MHz, CDCl₃) δ 11.14 (s, 1 H), 7.52 (d, J=9.2 Hz, 1H), 7.49-7.43 (m, 2H), 7.36-7.30 (m, 1H), 7.21-7.16 (m, 2H), 2.55 (d, J=2.3 Hz, 3H).

Step 2. Synthesis of Phenyl 2-(benzyloxy)-3-bromo-5-fluoro-6-methylbenzoate 78 from Phenyl 3-bromo-5-fluoro-2-hydroxy-6-methylbenzoate 77

Compound 77 (crude, 1.06 g, 2.97 mmol) was dissolved in acetone (20 mL) containing potassium carbonate (821 mg, 5.94 mmol, 2.0 equiv.) and the mixture was cooled to 0° C. in an ice-bath. Benzyl bromide (540 μL, 4.45 mmol, 1.5 equiv.) was added dropwise. After 2 hrs, LC/MS indicated that the starting material was consumed 40%. The reaction mixture was heated to 50° C. for another hour the cooled and diluted with ethyl acetate (100 mL), and successively washed with water and brine. The organics were dried over Na₂SO₄, filtered, and concentrated under reduced pressure to afford 2.2 g of crude 78, which was purified by column chromatography (Biotage 10 g column, 2 to 5% ethyl acetate in hexane gradient), yielding 1.03 g (84% for two steps) of the pure compound 78 as a colorless oil: ¹H NMR (400 MHz, CDCl₃) δ 7.50-7.47 (m, 2H), 7.40-7.33 (m, 6H), 7.25 (t, J=7.3 Hz, 1H), 7.04 (d, J=8.6 Hz, 2H), 5.09 (s, 2H), 2.32 (d, J=1.8 Hz, 3H).

Step 3. Synthesis of Phenyl 2-(benzyloxy)-3-bromo-5-fluoro-4-formyl-6-methylbenzoate 79 from Phenyl 2-(benzyloxy)-3-bromo-5-fluoro-6-methylbenzoate 78

A LDA solution was prepared by adding n-BuLi (1.6 M in hexane, 5.1 mL, 8.16 mmol, 1.5 equiv) to a solution of diisopropylamine (1.15 mL, 8.16 mmol) in THF (15 mL) at −78° C. The reaction mixture was warmed up to −20° C. and stirred for 15 min. Thr LDA solution was cooled again to −78° C. to which was added dropwise a solution of compound 78 (2.26 g, 5.44 mmol) in THF (5 mL), forming an orange-red solution. After 10 min, DMF (1.26 mL, 16.3 mmol, 3 equiv) was added dropwise. The reaction solution was allowed to warm up to −20° C. over 1 hour and was then quenched with NH₄Cl (saturated aqueous solution). The reaction mixture was diluted with ethyl acetate (100 mL) and washed with water and brine. The organics were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. This gave 2.42 g of the crude compound 79, which was purified by column chromatography (Biotage 24 g column, 5 to 10% ethyl acetate in hexane gradient), yielding 2.23 g (92%) of the pure compound 79 as light yellow solid. ¹H NMR (400 MHz, CDCl₃) δ 10.37 (s, 1H), 7.51-7.47 (m, 2H), 7.40-7.33 (m, 5H), 7.27 (t, J=7.3 Hz, 1H), 7.06-7.02 (m, 2H), 5.12 (s, 2H), 2.37 (d, J=2.3 Hz, 3H).

Step 4. Synthesis of Phenyl 2-(benzyloxy)-3-bromo-5-fluoro-4-(hydroxymethyl)-6-methylbenzoate 80 from Phenyl 2-(benzyloxy)-3-bromo-5-fluoro-4-formyl-6-methylbenzoate 79

Compound 79 (416 mg, 0.94 mmol) was dissolved in methanol (5 mL) and sodium borohydride (75.6 mg, 2 mmol) was added in several portions. After stirring at ambient temperature for 30 min, the reaction mixture was diluted with ethyl acetate and washed with water (2×20 mL) and brine. The organics were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The crude material was purified by column chromatography (Biotage 10 g column, 5 to 20% ethyl acetate in hexane gradient), yielding 367 mg (87.7%) of the pure compound 80 as a colorless oil. ¹H NMR (400 MHz, CDCl₃) δ 10.37 (s, 1H), 7.49 (dd, J=7.8, 2.3 Hz, 2H), 7.40-7.33 (m, 5H), 7.25 (t, J=7.8 Hz, 1H), 7.07-7.02 (m, 2H), 5.10 (s, 2H), 4.91 (dd, J=6.9, 2.3 Hz, 2H), 2.35 (d, J=2.3 Hz, 3H); MS (ESI) m/z 467.10, 469.08 (M+Na).

Step 5. Synthesis of Phenyl 2-(benzyloxy)-5-fluoro-3,4-bis(hydroxymethyl)-6-methylbenzoate 81 from Phenyl 2-(benzyloxy)-3-bromo-5-fluoro-4-(hydroxymethyl)-6-methylbenzoate 80

i-Propyl magnesium chloride/lithium chloride solution (1.2 M in THF, 4.4 mL, 5.3 mmol) was added to a −78° C. solution of compound 80 (472 mg, 1.06 mmol) in THF (10 mL). The reaction mixture was allowed to warm to 0° C. over 1 hour. Paraformaldehyde (318 mg, 10.6 mmol) was added, and the reaction was allowed to warm to ambient temperature. After 1 hour, the reaction mixture was heated to 40° C. then cooled, quenched with ammonium chloride (saturated aqueous solution) and extracted with EtOAc (2×). The combined extracts were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The crude material was purified by column chromatography (Biotage 10 g column, 10 to 35% EtOAc in hexane gradient), yielding 337 mg (80%) of compound 81 as a thick oil. ¹H NMR (400 MHz, CDCl₃) δ 7.45-7.34 (m, 7H), 7.30-7.23 (m, 1H), 7.10 (d, J=7.8 Hz, 2 H), 5.08 (s, 2H), 4.85 (s, 2H), 4.76 (s, 2H), 2.39 (d, J=2.3 Hz, 3H); MS (ESI) m/z 419.19 (M+Na).

Step 6. Synthesis of Phenyl 2-(benzyloxy)-3,4-bis(chloromethyl)-5-fluoro-6-methylbenzoate 82 from Phenyl 2-(benzyloxy)-5-fluoro-3,4-bis(hydroxymethyl)-6-methylbenzoate 81

To a solution of compound 81 (2.98 g, 7.52 mmol, 1 equiv) in dichloroethane (20 mL) was added thionyl chloride (2.18 mL, 30.1 mmol, 4 equiv) and tetrabutylammonium chloride (174 mg, 0.76 mmol, 0.1 equiv). The reaction vessel was sealed and the mixture was heated to 80° C. for 2 h before being concentrated under reduced pressure. Purification of the resulting crude oil via flash column chromatography on silica gel (Redisep, 80 g, 4 to 6% EtOAc in hexane gradient) provided 2.66 g of compound 82 (81%) as a waxy white solid: ¹H NMR (400 MHz, CDCl₃) δ 7.48-7.42 (m, 2H), 7.41-7.34 (m, 4H), 7.29-7.24 (m, 1H), 7.10-7.05 (m, 2H), 5/13 (s, 2H), 4.81 (s, 4H), 2.44-2.39 (m, 3H); MS (ESI) m/z 431.14, 433.16 (M+H).

Step 7. Synthesis of Phenyl 4-(benzyloxy)-2-tert-butyl-7-fluoro-6-methylisoindoline-5-carboxylate 83 from Phenyl 2-(benzyloxy)-3,4-bis(chloromethyl)-5-fluoro-6-methylbenzoate 82

Compound 82 (120 mg, 0.277 mmol), t-butylamine (0.032 mL, 0.305 mmol) and N,N-diisopropylethylamine (0.096 mL, 0.554 mmol) were heated to 110° C. in 1,2-dimethoxyethane (1 mL). After 2 hours, additional t-butylamine (0.100 mL, 0.95 mmol) was added. After 2 more hours, additional t-butylamine (0.500 mL, 4.75 mmol) was added, and the reaction mixture was heated overnight. The reaction mixture was concentrated under reduced pressure and was purified by column chromatography (Biotage 10 g column, 5 to 20% EtOAc in hexane gradient), yielding 64.1 mg (53%) of desired compound 83. R_(f)=0.25 in 20% EtOAc in hexane; ¹H NMR (400 MHz, CDCl₃) δ 7.42-7.30 (m, 7H), 7.27-7.20 (m, 1 H), 7.04 (d, J=7.8 Hz, 2H), 5.02 (s, 2H), 4.08 (s, 2H), 4.04 (s, 2H), 2.33 (d, J=1.8 Hz, 3 H), 1.15 (s, 9H); MS (ESI) m/z 434.29 (M+H).

Example 53 Preparation of Indoline analog 85 from Phenyl 4-(benzyloxy)-2-tert-butyl-7-fluoro-6-methylisoindoline-5-carboxylate 83

Step 1. Synthesis of protected indoline analog 84 from Phenyl 4-(benzyloxy)-2-tert-butyl-7-fluoro-6-methylisoindoline-5-carboxylate 83

To a solution of lithium diisopropylamide (2.0 M in hexanes, 125 μL, 0.25 mmol, 3.8 equiv) and TMEDA (49 μL, 0.33 mmol, 5 equiv) in THF (3 mL) at −70° C. was added dropwise a solution of compound 83 (54.0 mg, 0.125 mmol, 1.2 equiv) in THF (750 μL). After 20 min, a solution of compound 59 (32.2 mg, 0.065 mmol, 1 equiv) in THF (750 μL) was added, followed by slow warming to −5° C. over 1.5 h. Excess base was quenched by the addition of a saturated, aqueous solution of ammonium chloride (1 mL). The solution was warmed to ambient temperature, poured into a saturated, aqueous solution of ammonium chloride (5 mL) and water (3 mL) and extracted with EtOAc (2×30 mL). The combined organic extracts were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. Purification of the resulting oil via flash column chromatography on silica gel (Biotage 10 g, 3 to 25% EtOAc in hexanes gradient) provided compound 84 as a yellow oil: NMR (400 MHz, CDCl₃) δ 16.4 (s, 1H), 7.49-7.38 (m, 4H), 7.38-7.26 (m, 6H), 5.34 (s, 2H), 5.03 (d, J=10.4 Hz, 1H), 4.88 (d, J=10.4 Hz, 1H), 3.00-2.91 (m, 1H), 2.74-2.64 (m, 1H), 4.05-3.99 (m, 1H), 3.98-3.84 (m, 2H), 3.93-3.56 (m, 1H), 2.47 (s, 6H), 1.22 (s, 9H), 1.23 (t, J=7.3 Hz, 3H), 0.87 (s, 9H), 0.23 (s, 3H), 0.16 (s, 3H); MS (ESI) m/z 836.54 (M−H).

Step 2. Synthesis of Indoline Analog 85 from Protected Indoline Analog 84

To a solution of compound 84 (25 mg, 70% pure, ˜0.020 mmol, 1 equiv) in dioxane (750 μL) was added an aqueous solution of HF (50%, 200 μL). After 16 h, the reaction mixture was poured into an aqueous K₂HPO₄ solution (2.4 g in 25 mL) and extracted with EtOAc (2×30 mL). The combined organic layers were dried (Na₂SO₄), filtered, and concentrated under reduced pressure. Palladium on carbon (10%; 11 mg) was added to a solution of this crude oil in dioxane:MeOH:0.5 N HCl in MeOH (1:1:1, 1.5 mL). The flask was fitted with a septum and evacuated and back-filled three times with hydrogen gas. The reaction was stirred under an atmosphere of hydrogen gas for 85 min. The reaction mixture was filtered through celite to remove the palladium catalyst and then concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil provided 4.2 mg of the desired compound 85: ¹H NMR (400 MHz, CD₃OD) δ 4.91-4.85 (m, 2H), 4.79-4.74 (m, 2 H), 4.10 (s, 1H), 3.10-2.89 (m, 8H), 2.60 (d, J=16.5 Hz, 1H), 2.03 (dd, J=3.05, 14.0 Hz, 1H), 1.95-1.86 (m, 1H), 1.53 (s, 9H), 1.27 (d, J=4.9 Hz, 3H); MS (ESI) m/z 544.35 (M+H).

Example 54 Preparation of Pyridine analog 91 from 3,5-Dichloropyridine-4-carboxylic 86

Step 1. Synthesis of 3-(Benzyloxy)-5-chloropyridine-4-carboxylic acid 87 from 3,5-Dichloropyridine-4-carboxylic 86

Sodium hydride (60% dispersion in mineral oil, 4.37 g, 109 mmol) was added portionwise to a solution of 3,5-dichloroisonicotinic acid (10.24 g, 53.3 mmol) in NMP (100 mL). After gas evolution ceased, benzyl alcohol (5.52 mL, 53.3 mmol) was added dropwise. After gas evolution ceased, the reaction mixture was heated to 80° C. After 1 hour, the reaction was complete and was allowed to cool to RT and stand overnight. The reaction mixture was diluted with water (300 mL) and was washed with Et₂O (2×100 mL, discarded). The aqueous layer was brought to pH ˜2 with conc. HCl, causing a precipitate to form. The mixture was diluted with brine (100 mL) and was allowed to stand for 30 minutes. The solid was collected by filtration, washed with water (3×), and was dried in a 45° C. vacuum oven overnight. This gave 9.36 g (67%) of the product 87 as a white solid. ¹H NMR (400 MHz, DMSO-d6) δ 14.30-14.10 (bs, 1H), 8.52 (s, 1H), 8.34 (s, 1H), 7.50-7.30 (m, 5H), 5.33 (s, 2 H); MS (ESI) m/z 264.20 (M+H).

Step 2. Synthesis of Phenyl 3-(benzyloxy)-5-chloropyridine-4-carboxylate 88 from 3-(Benzyloxy)-5-chloropyridine-4-carboxylic acid 87

Oxalyl chloride (4.9 mL, 56 mmol) was added to a suspension of compound 86 (3.71 g, 14.1 mmol) in CH₂Cl₂ (50 mL) over ˜2 minutes. DMF was added dropwise in 20 μL portions every 5 minutes until complete solution was achieved. After stirring for an additional 30 minutes, the reaction mixture was concentrated under reduced pressure. The resulting solid was dissolved in CH₂Cl₂ (50 mL) and phenol (2.65 g, 28.1 mmol), DMAP (0.172 g, 1.41 mmol), and Et₃N (9.76 mL, 70.4 mmol) were added sequentially. After 1 hour, the reaction mixture was diluted with CH₂Cl₂ (50 mL) and was washed with water (2×100 mL) and NaHCO₃ (saturated, aqueous, 100 mL). The organics were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The material was purified by column chromatography (Biotage 50 g column, 0 to 25% EtOAc in Hexanes gradient), yielding 4.20 g (88%) of compound 88 as an off-white solid. R_(f)=0.43 in 30% EtOAC/Hexanes. ¹H NMR (400 MHz, DMSO-d6) δ 8.70 (s, 1H), 8.48 (s, 1H), 7.52-7.30 (m, 8H), 7.15-7.08 (m, 2H), 5.44 (s, 2H); MS (ESI) m/z 340.25 (M+H).

Step 3. Synthesis of Phenyl 3-(benzyloxy)-5-methylpyridine-4-carboxylate 89 from Phenyl 3-(benzyloxy)-5-chloropyridine-4-carboxylate 88

Compound 88 (2.01 g, 5.92 mmol), methyl boronic acid (1.06 g, 17.7 mmol), dichlorobis(tricyclohexylphosphine)palladium(II) (102 mg, 0.296 mmol), and K₃PO₄ (3.76 g, 17.7 mmol) were heated to 100° C. in toluene (20 mL) and water (2 mL). After 16 hours, the reaction mixture was allowed to cool to ambient temperature, diluted with EtOAc (20 mL) and washed with water (20 mL) and brine (20 mL) before being dried over Na₂SO₄, filtered, and concentrated under reduced pressure. The material was purified by column chromatography (Biotage 50 g column, 0 to 40% EtOAc/Hexanes gradient), yielding 1.66 g (88%) of the compound 89 as a white solid. R_(f)=0.18 in 30% EtOAc/Hexanes. ¹H NMR (400 MHz, DMSO-d6) δ 8.50 (s, 1H), 8.26 (s, 1H), 7.52-7.30 (m, 8H), 7.20-7.10 (m, 2H), 5.37 (s, 2H), 2.38 (s, 3H); MS (ESI) m/z 320.27 (M+H).

Step 4. Synthesis of protected pyridine analog 90 from Phenyl 3-(benzyloxy)-5-methylpyridine-4-carboxylate 89

To a cooled (−70° C.) solution of lithium diisopropylamide (2.0 M in hexanes, 104 μL, 0.20 mmol, 4 equiv) and TMEDA (45 μL, 0.30 mmol, 6 equiv) in THF (1 mL) was added a solution of compound 89 (33.4 mg, 0.104 mmol, 2 equiv) in THF (500 μL). After 45 min, a solution of compound 59 (25 mg, 0.050 mmol, 1 equiv) in THF (500 μL) and the solution was allowed to warm up to −20° C. over 75 min. Excess base was quenched by the addition of a saturated, aqueous solution of ammonium chloride (1 mL). The solution was warmed to ambient temperature, poured into a saturated, aqueous solution of ammonium chloride (10 mL) and water (3 mL) and extracted with EtOAc (2×25 mL). The combined organic extracts were dried over Na₂SO₄, filtered, and concentrated under reduced pressure. Purification of the resulting oil via flash column chromatography on silica gel (Biotage 10 g, 9 to 80% EtOAc in hexanes gradient) provided compound 90 as a yellow oil (5 mg). MS (ESI) m/z 720.42 (M−H).

Step 5. Synthesis of Pyridine analog 91 from Phenyl 3-(benzyloxy)-5-methylpyridine-4-carboxylate 89

To a solution of compound 90 (5 mg) in dioxane (700 μL) was added an aqueous solution of HF (50%, 200 μL). After 4.5 h, the reaction mixture was poured into an aqueous K₂HPO₄ solution (2.4 g in 25 mL) and extracted with EtOAc (2×30 mL). The combined organic layers were dried (Na₂SO₄), filtered, and concentrated under reduced pressure. Palladium on carbon (10%; 11 mg) was added to a solution of this crude oil in dioxane:MeOH:0.5 N HCl in MeOH (1:1:1, 900 μL). The flask was fitted with a septum and evacuated and back-filled three times with hydrogen gas. The reaction was stirred under an atmosphere of hydrogen gas for 80 min. The reaction mixture was filtered through celite and concentrated under reduced pressure. Preparative reverse phase HPLC of the resulting oil using provided 0.79 mg of the desired compound 91: ¹H NMR (400 MHz, CD₃OD) δ 8.54 (s, 1H), 8.28 (s, 1H), 4.13 (s, 1H), 3.19-2.93 (m, 9H), 2.13-2.05 (m, 1H), 2.01-1.92 (m, 1H), 1.30 (s, 3H); MS (ESI) m/z 430.06 (M+H).

Example 55 Synthesis of Silyl Dienol Ether 92

To a stirred solution of the AB enone 12A (1.055 g, 2.19 mmol) in dry 1,2-dichloroethane (25 mL) under an atmosphere of Ar was added triethylamine (2.44 mL, 8.0 eq.) and t-butyldimethylsilyl trifluoromethanesulfonate (2.0 mL, 4.0 eq.). The resultant solution was heated to relux and stirred 16 h under an inert atmosphere. The reaction mixture was poured over NaHCO₃ sat. aq. (60 mL) and extracted with ethyl acetate (2×70 mL). The combined organics were washed with NaHCO₃ sat. aq., brine (60 mL), dried (Na₂SO₄), and concentrated in vacuo. Flash column chromatography (SiO₂, 10% ethyl acetate in hexanes) of the residue provided the silyl dienol ether 92 ((4aS,8aS,9S)-3-(benzyloxy)-5-((tert-butyldimethylsilypoxy)-9-(dimethylamino)-4-a-hydroxy-8a,9-dihydronaphtho[2,3-d]isoxazol-4(4aH)-one) as a waxy off-white solid (1.12 g, 86%): R_(f)=0.68 (20% ethyl acetate in hexanes); R_(f)=0.79 (20% ethyl acetate in hexanes); IR (neat) 2929, 1716, 1510, 1247 cm⁻¹; ¹H NMR (500 MHz, CDCl₃) δ 7.48 (d, J=7.8 Hz, 2H), 7.35 (m, 3H), 5.98 (dd, J=9.3, 5.9 Hz, 1H), 5.87 (dd, J=9.3, 5.9 Hz, 1H), 5.32 (m, 2H), 5.25 (d, J=5.8 Hz, 1H), 3.78 (d, J=10.3 Hz, 1H), 2.83 (dd, J=9.8, 5.9 Hz, 1H), 2.48 (s, 6H), 0.82 (s, 9H), 0.77 (s, 9H), 0.15 (s, 6H), 0.13 (s, 3H), −0.04 (s, 3H); ¹³C NMR (500 MHz, CDCl₃) δ 188.7, 181.8, 167.7, 151.0, 139.3, 135.1, 128.9, 128.5, 128.4, 123.0, 122.9, 107.9, 103.4, 94.7, 81.7, 72.3, 64.2, 48.1, 42.4, 25.8, 25.4, 18.9, 17.8, −2.8, −3.4, −4.5, −5.3; HRMS for C₃₂H₄₈N₂O₅Si₂ [MH+] m/z calc. 597.31745, found 596.31789.

Example 56 Synthesis of C5-Bromoenone 93

To a stirred solution of the silyl dienol ether 92 (3.048 g, 5.11 mmol) in THF (40 mL) with H₂O (10 mL) was added N-bromosuccinimide (1.09 g, 6.13 mmol, 1.2 eq.) which dissolved over approximately two minutes, at which point the reaction was determined to be complete (TLC monitoring). The reaction mixture was poured over NaHCO₃ sat. aq. (100 mL) and extracted with ethyl acetate (2×120 mL). The combined organics were washed with brine (100 mL), dried (Na₂SO₄), and concentrated in vacuo. Flash column chromatography (SiO₂, 20% ethyl acetate in hexanes) of the residue provided the bromoenone 93 ((4aS,8R,8aS,9S)-3-(benzyloxy)-8-bromo-4-a-((tert-butyldimethylsilyl)oxy)-9-(dimethylamino)-8a,9-dihydronaphtho[2,3-d]isoxazole-4,5(4aH,8H)-dione) as a yellow solid (2.456 g, 86%): R_(f)=0.50 (20% ethyl acetate in hexanes); IR (neat) 2935, 1722, 1688, 1616, 1514, 1473 cm⁻¹; ¹H NMR (500 MHz, CDCl₃) δ 7.50 (d, J=6.8 Hz, 2H), 7.37 (m, 3H), 6.88 (m, 1H), 6.10 (d, J=10.2 Hz, 1H), 5.37 (s, 2H), 5.34 (d, J=4.4 Hz, 1H), 3.55 (d, J=10.7 Hz, 1H), 3.22 (d, J=10.7 Hz, 1H), 2.52 (s, 6H), 0.94 (s, 9H), 0.22 (s, 3H), 0.06 (s, 3H); ¹³C NMR (500 MHz, CDCl₃) δ 193.3, 186.3, 179.4, 167.4, 145.1, 134.9, 128.6, 128.6, 128.4, 127.3, 82.7, 72.7, 60.8, 53.0, 42.0, 38.2, 26.4, 19.3, 17.8, 12.3, −2.4, −2.7; HRMS for C₂₆H₃₃N₂O₅SiBr [MH+] m/z calc. 561.14149, found 561.14899.

Example 57 Synthesis of Azidoenone 94

To a stirred solution of the bromoenone 93 (790 mg, 1.41 mmol) in dry acetonitrile (12 mL) under an atmosphere of Ar at room temperature was added tetramethylguanidinium azide (660 mg, 5.64 mmol, 4.0 eq.). After 30 min, the mixture was added dropwise via cannula to methyl t-butyl ether (200 mL). The mixture was dried (Na₂SO₄), filtered over Celite, and the filtrate was concentrated in vacuo. Flash column chromatography (SiO₂, 10% ethyl acetate in hexanes) of the residue provided the azidoenone 94 ((4aS,8S,8aR,9S)-8-azido-3-(benzyloxy)-4-a-((tert-butyldimethylsilyl)oxy)-9-(dimethylamino)-8a,9-dihydronaphtho[2,3-d]isoxazole-4,5(4aH,8H)-dione) as a pink powder which could be recrystallized from hot hexanes (412 mg, 60%) to off-white needles: R_(f)=0.68 (20% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDCl₃) δ 7.49 (d, J=7.0 Hz, 2H), 7.37 (m, 3H), 6.72 (dd, J=8.0, 6.5 Hz, 1H), 6.10 (dd, J=10.5, 3.0 Hz, 1H), 5.34 (s, 2H), 5.18 (m, 1H), 4.04 (d, J=8.5 Hz, 1H), 3.12 (m, 1H), 2.44 (s, 6H), 0.86 (s, 9H), 030 (s, 3H), 0.05 (s, 3H); ¹³C NMR (500 MHz, CDCl₃) δ 190.9, 185.6, 179.8, 166.9, 147.9, 134.8, 128.6, 128.5, 128.5, 128.4, 108.9, 83.4, 72.6, 58.0, 57.9, 51.5, 41.2, 31.2, 29.7, 26.0, 18.9, 1.0, −2.4, −3.9; HRMS for C₂₆H₃₃N₅O₅Si [MH+] m/z calc. 524.23237, found 524.23489.

Example 58 Synthesis of C5-Michael-Claisen Product 96

To a stirred suspension of azidoenone 94 (345 mg, 0.659 mmol) in methanol (10 mL) was added anhydrous stannous chloride (375 mg, 1.97 mmol, 3.0 eq.). The mixture was stirred 12 h at 23° C. and concentrated in vacuo. The residue was suspended between methyl t-butyl ether (10 mL) and 0.5 M NaOH aq. (15 mL) and stirred vigorously until both layers were clear. The organic layer was collected and the aqueous layer was further extracted with methyl t-butyl ether (3×10 mL). The combined organics were dried (Na₂SO₄) and concentrated to provide the intermediate aminoenone as a gray solid, pure by ¹H NMR. The intermediate amine was dissolved in dry acetonitrile (4 mL) under an atmosphere of Ar. To this was added triethylamine (450 μL, 3.23 mmol, 5.0 eq.) and t-butyldiphenylsilyl chloride (339 μL, 1.30 mmol, 2.02 eq.) and the mixture stirred 1 h. The reaction mixture was diluted in methyl t-butyl ether (25 mL) and washed with 0.5M NaOH aq. (2×20 mL), brine (20 mL), dried (Na₂SO₄) and concentrated in vacuo to the desired bis-silylated aminoenone as a brown oil, pure by ¹H NMR, and was used without further purification.

A solution of lithium diisopropylamide (LDA, 0.5M in THF) was prepared immediately prior to its use and kept under an atmosphere of Ar (g). To a stirred solution of compound 95 (880 mg, 2.58 mmol, 4.0 eq.) in dry THF (12 mL) with dry TMEDA (distilled from CaH₂, 423 μL, 2.84 mmol, 4.4 eq.) under an atmosphere of Ar (g) at −78° C. was added LDA (5.7 mL, 2.84 mmol, 4.4 eq.). After allowing to stir 30 min at −78° C., during which time the solution became a deep red color, the crude bis-silylated aminoenone (0.645 mmol, 1.0 eq.) was added as a solution in dry THF (4 mL) and the mixture was stirred an additional 40 min. The reaction was slowly warmed to −10° C. over 2 hrs, at which point it was quenched by the addition of pH=7 buffer. The aqueous layer was adjusted to pH=7, then extracted with dichloromethane (2×20 mL) and the organic layer dried (Na₂SO₄) and concentrated. Flash column chromatography (SiO₂, 20% ethyl acetate in hexanes) of the residue provided the Michael-Claisen product 96 ((4aS,11R,11aR,12S,12aR,13S)-3-(benzyloxy)-4-a-((tert-butyldimethylsilyl)oxy)-12-((tert-butyldiphenylsilyl)amino)-13-(dimethylamino)-5-hydroxy-11-methyl-4,6-dioxo-4,4-a,6,11,11a,12,12a,13-octahydrotetraceno[2,3-d]isoxazol-7-yl tert-butyl carbonate) (411 mg, 65% for three steps) as a bright yellow foam: R_(f)=0.57 (30% ethyl acetate in hexanes); IR (neat) 2929, 1759, 1716, 1604, 1510, 1147 cm⁻¹; ¹H NMR (500 MHz, CDCl₃) δ 17.33 (s, 1H), 7.28-7.54 (m, 16H), 7.05 (dd, J=7.8, 6.4 Hz, 2H), 5.44 (q, J=8.2 Hz, 2H), 3.60 (s, 1H), 3.35 (d, J=12.2 Hz, 1H), 3.16 (m, 1H), 2.75 (dd, J=8.3, 3.0 Hz, 1H) 2.35 (s, 1H), 2.21 (s, 6H), 1.60 (m, 1H), 1.58 (s, 9H), 0.81 (s, 9H), 0.70 (bs, 3H), 0.60 (s, 3H), −0.10 (s, 3H); ¹³C NMR (500 MHz, CDCl₃) δ 193.4, 188.2, 184.3, 180.7, 167.8, 151.6, 150.4, 147.7, 146.8, 136.3, 136.3, 135.2, 134.9, 134.0, 133.7, 129.9, 129.3, 128.4, 128.4, 127.9, 127.3, 124.0, 122.7, 121.9, 114.3, 108.3, 105.6, 97.4, 83.4, 72.1, 61.3, 54.2, 52.6, 45.1, 42.2, 31.9, 27.7, 27.2, 25.7, 18.9, 18.8, 17.0, −3.1, −3.2; HRMS for C₅₆H₆₉N₃O₉Si₂ [MH+] m/z calc. 984.46451, found 984.46680.

Example 59 Synthesis of C5-5-amino-6-deoxytetracycline 97

Concentrated aqueous hydrofluoric acid solution (48 wt %, 1.5 mL) was degassed with bubbling Ar and added to a degassed (Ar) solution of the Michael-Claisen product 96 (9.1 mg, 0.0089 mmol) in acetonitrile (1.5 mL) in a polypropylene reaction vessel at 23° C. The reaction solution was stirred vigorously under an atmosphere of Ar at 23° C. for 36 h. To this mixture was added a suspension of palladium on activated carbon (10 wt %, 22 mg) in methanol (degassed with bubbling Ar) in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The yellow reaction mixture was stirred at 23° C. for 1 h, then was cooled in a 4° C. bath and quenched by the dropwise addition of methoxytrimethylsilane until bubbling ceased. The mixture was filtered through a syringe filter and the filtrate concentrated, providing a yellow solid. The product was purified by preparatory HPLC using an Agilent C18 column [10 μM, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% TFA aq., Solvent B: acetonitrile, isochratic elution 15% B, flow rate: 15 mL/min]. Fractions eluting at 39 min were collected and concentrated, affording 5-aminodoxycycline trifluoracetate 97 as a pale yellow powder (2.2 mg, 57% for two steps): ¹H NMR (500 MHz, CD₃OD) δ 7.47 (t, J=8.0, 7.5 Hz, 1H), 7.00 (d, J=7.5 Hz, 1H), 6.82 (d, J=8.0 Hz, 1H), 4.49 (s, 1H), 4.18 (d, J=10.0 Hz, 1H), 2.8-3.12 (m, 3H), 3.10 (s, 6H), 1.49 (d, J=6.0 Hz, 3H); HRMS for C₂₂H₂₅N₃O₇ [MH+] m/z calc. 444.17653, found 444.17616.

Example 60 Synthesis of C5-Substituted Enones 98 and 99

To a stirred solution of the silyl dienol ether 92 (362 mg, 0.652 mmol) in 1,2-dichloroethane (10 mL) was added Eschenmoser's salt (150 mg, 0.80 mmol, 1.2 eq.). The mixture was heated to reflux and stirred 14 h. After cooling to room temperature, the solution was diluted in CH₂Cl₂ (25 mL) and washed with sat. aq. NaHCO₃ (2×25 mL), the organic layer was dried (Na₂SO₄) and concentrated in vacuo. Flash column chromatography (SiO₂, 20% ethyl acetate in hexanes to elute enone 99 ((4aS,8aS,9S)-3-(benzyloxy)-4-a-((tert-butyldimethylsilyl)oxy)-9-(dimethylamino)-8-methylene-8a,9-dihydronaphtho[2,3-d]isoxazole-4,5(4aH,8H)-dione (B)), and flushing with ethyl acetate to elute enone 98 ((4aS,8R,8aS,9S)-3-(benzyloxy)-4-a-((tert-butyldimethylsilyl)oxy)-9-(dimethylamino)-8-((dimethylamino)methyl)-8a,9-dihydronaphtho[2,3-d]isoxazole-4,5(4aH,8H)-dione (A)) of the residue provided the products 98 (139 mg, 40%) as a bright yellow oil and 99 (154 mg, 48%) as an orange solid: Enone 98: R_(f)=0.05 (20% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDCl₃) δ 7.52 (d, J=6.9 Hz, 2H), 7.41 (dd, J=7.8, 6.8 Hz, 2H), 7.36 (d, J=7.3 Hz, 1H), 6.92 (m, 1H), 6.10 (dd, J=10.2, 1.9 Hz, 1H), 5.38 (s, 2H), 3.59 (d, J=11.3 Hz, 1H), 3.21 (m, 1H), 2.92 (d, J=12.2 Hz, 1H), 2.80 (dd, J=11.7, 8.8 Hz, 1H), 2.56 (dd, J=12.2, 6.3 Hz, 1H), 2.50 (s, 6H), 2.28 (s, 6H), 0.90 (s, 9H), 0.26 (s, 3H), 0.03 (s, 3H); Enone 99: R_(f)=0.52 (20% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDCl₃) δ 7.52 (d, J=7.4 Hz, 2H), 7.41 (dd, J=7.4, 5.9 Hz, 2H), 7.37 (d, J=5.9 Hz, 1H), 7.13 (d, J=10.3 Hz, 1H), 6.00 (d, J=10.3 Hz, 1H), 5.64 (s, 1H), 5.52 (s, 1H), 5.38 (s, 2H), 3.74 (d, J=10.3 Hz, 1H), 3.27 (d, J=10.3 Hz, 1H), 2.48 (s, 6H), 0.80 (s, 9H), 0.24 (s, 3H), 0.07 (s, 3H).

Example 61 Synthesis of C5-Michael-Claisen Product 100

A solution of lithium diisopropylamide (LDA, 0.5M in THF) was prepared immediately prior to its use and kept under an atmosphere of Ar (g). To a stirred solution of phenylester 34 (59 mg, 0.160 mmol, 4.0 eq.) in dry THF (3 mL) with dry TMEDA (distilled from CaH₂, 26 μL, 0.176 mmol, 4.4 eq.) under an atmosphere of Ar (g) at −78° C. was added LDA (352 μL, 0.176 mmol, 4.4 eq.). After allowing to stir 30 min at −78° C., during which time the solution became a deep red color, enone 99 (20 mg, 0.040 mmol, 1.0 eq.) was added as a solution in dry THF (1 mL) and the mixture was stirred an additional 40 min. The reaction was slowly warmed to −10° C. over 1.5 hrs, at which point it was quenched by the addition of pH 7 buffer. The pH of the aqueous layer was adjusted to 7, which was then extracted with dichloromethane (3×25 mL) and the organic layer dried (Na₂SO₄) and concentrated. Flash column chromatography (SiO₂, 20% ethyl acetate in hexanes, then 50% ethyl acetate in hexanes) of the residue provided the Michael-Claisen product 100 ((4aS,11aS,12aS,13S)-3-(benzyloxy)-4-a-((tert-butyldimethylsilypoxy)-10,13-bis(dimethylamino)-5-hydroxy-12-methylene-4,6-dioxo-4,4-a,6,11,11a,12,12a,13-octahydrotetraceno[2,3-d]isoxazol-7-yl tert-butyl carbonate) (17.0 mg, 57%) as a bright yellow oil: R_(f)=0.17 (15% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDCl₃) δ 15.65 (s, 1H), 7.50 (d, J=7.4 Hz, 2H), 7.40 (dd, J=7.4, 6.8 Hz, 2H), 7.35 (d, J=7.4 Hz, 1H), 7.25 (d, J=8.8 Hz, 1H), 7.05 (d, J=8.8 Hz, 1H), 5.42 (s, 1H), 5.37 (s, 2H), 5.22 (s, 1H), 4.18 (d, J=10.7 Hz, 1H), 3.51-3.62 (m, 2H), 3.49 (s, 1H), 3.15 (d, J=10.3 Hz, 1H), 2.66 (s, 6H), 2.53 (s, 6H), 1.55 (s, 9H), 0.77 (s, 9H), 0.26 (s, 3H), 0.10 (s, 3H); ¹³C NMR (500 MHz, CDCl₃) 8186.4, 184.4, 181.6, 180.4, 167.7, 152.1, 149.8, 145.3, 140.6, 136.6, 134.9, 128.5, 128.4, 128.4, 124.1, 123.9, 122.2, 119.1, 108.3, 106.7, 83.7, 81.9, 72.5, 61.0, 6.0, 53.4, 44.1, 41.6, 36.4, 34.5, 30.8, 27.6, 25.8, 18.9, −2.6, −3.9.

Example 62 Synthesis of C5-methylene-minocycline 101

Concentrated aqueous hydrofluoric acid solution (48 wt %, 1.5 mL) was added to a solution of the Michael-Claisen product 100 (17 mg, 0.022 mmol) in acetonitrile (1.5 mL) in a polypropylene reaction vessel at 23° C. The reaction solution was stirred vigorously at 23° C. for 30 h, then was poured into aq. K₂HPO₄ and adjusted to pH=7. The resulting mixture was extracted with ethyl acetate (3×25 mL). The organic extracts were combined and the combined solution was dried (Na₂SO₄) and concentrated, affording a yellow solid. Methanol (4 mL) was added to the crude product, forming a yellow solution. Palladium on activated carbon (10 wt %, 22 mg) was added in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The yellow reaction mixture was stirred at 23° C. for 20 min, then was filtered through a syringe filter plug. The filtrate was concentrated, providing a yellow solid. The product was purified by preparatory HPLC in using an Agilent C18 column [10 μM, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% TFA aq., Solvent B: acetonitrile, gradient elution 5→35% B over 40 min, flow rate: 10 mL/min]. Fractions eluting at 24-25 min were collected and concentrated, affording 5-methyleneminocycline trifluoracetate 101 as a pale yellow powder (1.7 mg, 17% for two steps): ¹H NMR (500 MHz, CD₃OD) δ 7.67 (d, J=8.8 Hz, 1H), 6.95 (d, J=9.3 Hz, 1H), 5.62 (bs, 1H), 5.45 (bs, 1H), 4.65 (bs, 1H), 3.78 (bs, 1H), 3.57 (d, J=5.4 Hz, 1H), 3.07 (s, 6H), 3.02-3.17 (m, 2H), 2.93 (s, 6H); HRMS for C₂₄H₂₇N₃O₇ [MH+] m/z calc. 470.19218, found 470.19163.

Example 63 Synthesis of C5-Michael-Claisen Product 102

A solution of lithium diisopropylamide (LDA, 0.5M in THF) was prepared immediately prior to its use and kept under an atmosphere of Ar (g). To a stirred solution of phenylester 34 (59 mg, 0.160 mmol, 4.0 eq.) in dry THF (3 mL) with dry TMEDA (distilled from CaH₂, 26 μL, 0.176 mmol, 4.4 eq.) under an atmosphere of Ar (g) at −78° C. was added LDA (352 μL, 0.176 mmol, 4.4 eq.). After allowing to stir 30 min at −78° C., during which time the solution became a deep red color, enone 98 (22 mg, 0.040 mmol, 1.0 eq.) was added as a solution in dry THF (1 mL) and the mixture was stirred an additional 40 min. The reaction was slowly warmed to −10° C. over 1.5 hrs, at which point it was quenched by the addition of pH 7 buffer. The pH of the aqueous layer was adjusted to 7, which was then extracted with dichloromethane (3×25 mL) and the organic layer dried (Na₂SO₄) and concentrated. Flash column chromatography (SiO₂, 20% ethyl acetate in hexanes, then 50% ethyl acetate in hexanes) of the residue provided the Michael-Claisen product 102 ((4aS,11aS,12R,12aS,13S)-3-(benzyloxy)-4-a-((tert-butyldimethylsilyl)oxy)-10,13-bis(dimethylamino)-12-((dimethylamino)methyl)-5-hydroxy-4,6-dioxo-4,4-a,6,11,11a,12,12a,13-octahydrotetraceno[2,3-d]isoxazol-7-yl tert-butyl carbonate) (25.0 mg, 78%) as a bright yellow oil: R_(f)=0.55 (50% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDCl₃) δ 15.69 (s, 1H), 7.52 (d, J=6.9 Hz, 2H), 7.42 (dd, J=7.4, 6.9 Hz, 2H), 7.38 (d, J=7.4 Hz, 1H), 7.25 (d, J=8.8 Hz, 1H), 7.03 (d, J=8.8 Hz, 1H), 5.39 (s, 2H), 3.71 (d, J=11.2 Hz, 1H), 3.54 (dd, J=15.1, 5.4 Hz, 1H), 2.99 (d, J=11.2 Hz, 1H), 2.82 (d, J=10.7 Hz, 1H), 2.71 (s, 6H), 2.67 (m, 1H), 2.51 (s, 6H), 2.38 (m, 1H), 2.29 (t, J=5.4 Hz, 1H), 2.26 (s, 6H), 1.55 (s, 9H), 0.91 (s, 9H), 0.25 (s, 3H), −0.01 (s, 3H).

Example 64 Synthesis of C5-dimethylaminomethylminocycline 103

Concentrated aqueous hydrofluoric acid solution (48 wt %, 1.5 mL) was added to a solution of the Michael-Claisen product 102 (25 mg, 0.031 mmol) in acetonitrile (1.5 mL) in a polypropylene reaction vessel at 23° C. The reaction solution was stirred vigorously at 23° C. for 30 h, then was poured into aq. K₂HPO₄ and adjusted to pH=7. The resulting mixture was extracted with ethyl acetate (3×25 mL). The organic extracts were combined and the combined solution was dried (Na₂SO₄) and concentrated, affording a yellow solid. Methanol (4 mL) was added to the crude product, forming a yellow solution. Palladium on activated carbon (10 wt %, 22 mg) was added in one portion at 23° C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The yellow reaction mixture was stirred at 23° C. for 20 min, then was filtered through a syringe filter plug. The filtrate was concentrated, providing a yellow solid. The product was purified by preparatory HPLC in using an Agilent C18 column [10 μM, 250×21.2 mm, UV detection at 350 nm, Solvent A: 0.1% TFA aq., Solvent B: acetonitrile, gradient elution 5-35% B over 40 min, flow rate: 10 mL/min]. Fractions eluting at 30-32 min were collected and concentrated, affording 5-dimethylaminomethylminocycline trifluoracetate 103 as a pale yellow powder (13.7 mg, 70% for two steps): ¹H NMR (500 MHz, CD₃OD) δ 7.86 (d, J=9.3 Hz, 1H), 7.04 (d, J=9.3 Hz, 1H), 5.62 (bs, 1H), 5.45 (bs, 1H), 4.65 (bs, 1H), 3.74 (dd, J=11.2, 10.7 Hz, 1H), 3.65 (d, J=10.7 Hz, 1H), 3.60 (dd, J=11.3, 6.9 Hz, 1H), 3.39 (dd, J=13.2, 4.9 Hz, 1H), 3.23 (s, 6H), 3.00 (bs, 6H), 2.89 (m, 1H), 2.62 (s, 6H), 2.61 (m, 1H), 2.32 (m, 1H); HRMS for C₂₆H₃₄N₄O₇ [MH+] m/z calc. 515.25003, found 515.24919.

Example 65 Antibacterial Activity

The antibacterial activities for the compounds of the invention were studied according to the following protocols, and are shown in FIGS. 1-7.

Minimum Inhibitory Concentration (MIC) Assay

MICs were determined according to the Clinical and Laboratory Standards Institute (CLSI) guidances (e.g., CLSI. Performance standards for antimicrobial susceptibility testing; nineteenth information supplement. CLSI document M100-S19, CLSI, 940 West Valley Road, Suite 1400, Wayne, Pa. 19087-1898, USA, 2009). Briefly, frozen bacterial strains were thawed and subcultured onto Mueller Hinton Broth (MHB) or other appropriate media (Streptococcus requires blood and Haemophilus requires hemin and NAD). Following incubation overnight, the strains were subcultured onto Mueller Hinton Agar and again incubated overnight. Colonies were observed for appropriate colony morphology and lack of contamination. Isolated colonies were selected to prepare a starting equivalent to a 0.5 McFarland standard. The inoculum was diluted 1:125 using MHB for further use. Test compounds were prepared by dilution in sterile water to a final concentration of 5.128 mg/mL. Antibiotics (stored frozen, thawed and used within 3 hours of thawing) and compounds were further diluted to the desired working concentrations.

The assays were run as follows. Fifty μL of MHB was added to wells 2-12 of a 96-well plate. One hundred μL of appropriately diluted antibiotics was added to well 1. Fifty μL of antibiotics was removed from well 1 and added to well 2 and the contents of well 2 mixed by pipetting up and down five times. Fifty μL of the mixture in well 2 was removed and added to well 3 and mixed as above. Serial dilutions were continued in the same manner through well 12. Fifty μL was removed from well 12 so that all contained 50 μL. Fifty μL of the working inoculum was then added to all test wells. A growth control well was prepared by adding 50 μL of working inoculum and 50 uL of MHB to an empty well. The plates were then incubated at 37° C. overnight, removed from the incubator and each well was read on a plate reading mirror. The lowest concentration (MIC) of test compound that inhibited the growth of the bacteria was recorded.

Example

1 2 3 4 5 6 7 8 9 10 11 12 [Abt] 32 16 8 4 2 1 0.5 0.25 0.125 0.06 0.03 0.015 grow − − − − − + + + + + + + [Abt] = antibiotic concentration in the well grow = bacterial growth (cloudiness) Interpretation: MIC = 2 μg/mL

Example 66 Protocol for Determining Inoculum Concentration (Viable Count)

Ninety μl of sterile 0.9% NaCl was pipetted into wells 2-6 of a 96-well microtiter plate. Fifty 50 μL of the inoculum was pipetted into well 1. Ten μL from was removed from well 1 and added it to well 2 followed by mixing. Ten μL was removed from well two and mixed with the contents of well 3 and so on creating serial dilutions through well 6. Ten μL was removed from each well and spotted onto an appropriate agar plate. The plate was placed into an incubator overnight. The colonies in spots that contain distinct colonies were counted. Viable count was calculated by multiplying the number of colonies by the dilution factor.

Spot from Well 1 2 3 4 5 6 Dilution Factor 10² 10³ 10⁴ 10⁵ 10⁶ 10⁷

Bacterial Strains

The following bacterial strains, listed below and in FIGS. 2-7, were examined in minimum inhibitory concentration (MIC) assays.

STRAIN ORGANISM DESIGNATION KEY PROPERTIES Staphylococcus aureus SA100 ATCC 13709, MSSA, Smith strain Staphylococcus aureus SA101 ATCC 29213, CLSI quality control strain, MSSA Staphylococcus aureus SA191 HA-MRSA, tetracycline-resistant, lung infection model isolate Staphylococcus aureus SA161 HA-MRSA, tetracycline-resistant, tet(M) Staphylococcus aureus SA158 Tetracycline-resistant tet(K) Staphylococcus epidermidis SE164 ATCC 12228, CLSI quality control strain, tetracycline-resistant Enterococcus faecalis EF103 ATCC 29212, tet-I/R, control strain Enterococcus faecalis EF159 Tetracycline-resistant, tet(M) Enterococcus faecalis EF327 Wound isolate (US) tet(M) Enterococcus faecium EF404 Blood isolate (US) tet(M) Streptococcus pneumoniae SP106 ATCC 49619, CLSI quality control strain Streptococcus pneumoniae SP160 Tetracycline-resistant, tet(M) Streptococcus pyogenes SP312 2009 clinical isolate, tet(M) Streptococcus pyogenes SP193 S. pyogenes for efficacy models; tetS; sensitive to sulfonamides Haemophilus influenzae HI262 Tetracycline-resistant, ampicillin-resistant Moraxella catarrhalis MC205 ATCC 8176, CLSI quality control strain Escherichia coli EC107 ATCC 25922, CLSI quality control strain Escherichia coli EC155 Tetracycline-resistant, tet(A) Escherichia coli EC878 MG1655 tolC::kan Escherichia coli EC880 lpxA Escherichia coli EC882 impA Escherichia coli EC200 MDR uropathogenic; serotype O17:K52:H18; UMN 026; trimeth/sulfa-R; BAA-1161 Enterobacter cloacae EC108 ATCC 13047, wt Enterobacter cloacae EC603 Urine isolate (Spain) Klebsiella pneumoniae KP109 ATCC 13883, wt Klebsiella pneumoniae KP153 Tetracycline-resistant, tet(A), MDR, ESBL⁺ Klebsiella pneumoniae KP457 2009 ESBL⁺, CTX-M, OXA Proteus mirabilis PM112 ATCC 35659 Proteus mirabilis PM385 Urine ESBL⁺ isolate Pseudomonas aeruginosa PA111 ATCC 27853, wt, control strain Pseudomonas aeruginosa PA169 Wt, parent of PA170-173 Pseudomonas aeruginosa PA173 PA170 ΔmexX; MexXY-(missing a functional efflux pump) Pseudomonas aeruginosa PA555 ATCC BAA-47, wild type strain PAO1 Pseudomonas aeruginosa PA556 Multiple-Mex efflux pump knockout strain Pseudomonas aeruginosa PA689 Blood isolate (US) Acinetobacter baumannii AB110 ATCC 19606, wt Acinetobacter baumannii AB250 Cystic fibrosis isolate, MDR Stenotrophomonas maltophilia SM256 Cystic fibrosis isolate, MDR Burkholderia cenocepacia BC240 Cystic fibrosis isolate, MDR *MDR, multidrug-resistant; MRSA, methicillin-resistant S. aureus; MSSA, methicillin-sensitive S. aureus; HA-MRSA, hospital-associated MRSA; tet(K), major gram-positive tetracycline efflux mechanism; tet(M), major gram-positive tetracycline ribosome-protection mechanism; ESBL⁺, extended spectrum β-lactamase

Other Embodiments

The foregoing has been a description of certain non-limiting preferred embodiments of the invention. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims. 

1. A compound of formula:

or a pharmaceutically acceptable salt thereof; wherein

represents a single or double bond; R₁ and R₂ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(A); —CH₂OR_(A); —CH₂R_(A); —CH₂N(R_(A))₂; ═C(R_(A))₂; —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —N₃; —NO₂; —N(R_(A))₂; —NHC(O)R_(A); —NHSO₂R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₁ and R₂ are taken together to form ═O; R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₃ and R₄ are taken together to form ═O; R₅, R₇, R₉, R₁₀, and R₁₁ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₆ and R₈ are absent if the dashed line between the carbon atoms which R₆ and R₈ are attached to represents a bond, or are each independently hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —N₃; —NO₂, amino, alkylamino, or dialkylamino; each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀, and R₁₁ are not simultaneously hydrogen.
 2. (canceled)
 3. The compound of claim 1 of formula:

4-5. (canceled)
 6. The compound of claim 1 of formula:

or a pharmaceutically acceptable salt thereof; wherein

represents a single or double bond; R₁ and R₂ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(A); —CH₂OR_(A); —CH₂R_(A); —CH₂N(R_(A))₂; ═C(R_(A))₂; —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —N₃; —NO₂; —N(R_(A))₂; —NHC(O)R_(A); —NHSO₂R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₁ and R₂ are taken together to form ═O; R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₃ and R₄ are taken together to form ═O; R₅ and R₇ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₆ and R₈ are absent if the dashed line between the carbon atoms which R₆ and R₈ are attached to represents a bond, or are each independently hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —N₃; —NO₂, amino, alkylamino, or dialkylamino; R₁₀ is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and n is an integer in the range of 0 to 8, inclusive.
 7. The compound of claim 1 of formula:

or a pharmaceutically acceptable salt thereof; wherein

represents a single or double bond; R₁ and R₂ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(A); —CH₂OR_(A); —CH₂R_(A); —CH₂N(R_(A))₂; ═C(R_(A))₂; —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —N₃; —NO₂; —N(R_(A))₂; —NHC(O)R_(A); —NHSO₂R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₁ and R₂ are taken together to form ═O; R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₃ and R₄ are taken together to form ═O; R₅ and R₇ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₆ and R₈ are absent if the dashed line between the carbon atoms which R₆ and R₈ are attached to represents a bond, or are each independently hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —N₃; —NO₂, amino, alkylamino, or dialkylamino; R₁₁ is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and n is an integer in the range of 0 to 8, inclusive.
 8. The compound of claim 1 of formula:

or a pharmaceutically acceptable salt thereof; wherein

represents a single or double bond; R₁ and R₂ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(A); —CH₂OR_(A); —CH₂R_(A); —CH₂N(R_(A))₂; ═C(R_(A))₂; —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —N₃; —NO₂; —N(R_(A))₂; —NHC(O)R_(A); —NHSO₂R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₁ and R₂ are taken together to form ═O; R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₃ and R₄ are taken together to form ═O; R₅ and R₇ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₆ and R₈ are absent if the dashed line between the carbon atoms which R₆ and R₈ are attached to represents a bond, or are each independently hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —N₃; —NO₂, amino, alkylamino, or dialkylamino; R₉ is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and n is an integer in the range of 0 to 8, inclusive.
 9. The compound of claim 1, wherein R₁ is hydrogen or C₁₋₆ alkyl. 10-12. (canceled)
 13. The compound of claim 1, wherein R₂ is —H or C₁₋₆ alkyl. 14-38. (canceled)
 39. The compound of claim 1 of the formula:

wherein R_(C) is hydrogen or C₁-C₆ alkyl; and n is an integer in the range of 0 to 3, inclusive.
 40. The compound of claim 1 of the formula:

41-88. (canceled)
 89. The compound of claim 1 selected from the group consisting of:


90. The compound of claim 1 selected from the group consisting of:


91. The compound of claim 1 of formula:


92. The compound of claim 1 of formula:


93. The compound of claim 1 of formula:


94. A compound of formula:

or a pharmaceutically acceptable salt thereof; wherein X is —N(R₁)—, —S—, or —O—;

represents a single or double bond; R₁ is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(A); —CH₂OR_(A); —CH₂R_(A); —CH₂N(R_(A))₂; ═C(R_(A))₂; —C(═O)R_(A); —CO₂R_(A); —CN; —SCN; —SR_(A); —SOR_(A); —SO₂R_(A); —N₃; —NO₂; —N(R_(A))₂; —NHC(O)R_(A); —NHSO₂R_(A); or —C(R_(A))₃; wherein each occurrence of R_(A) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₃ and R₄ are taken together to form ═O; R₅, R₇, R₉, R₁₀, and R₁₁ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₆ and R₈ are absent if the dashed line between the carbon atoms which R₆ and R₈ are attached to represents a bond, or are each independently hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, substituted or unsubstituted alkoxy, —OH, —CN, —SCN, —SH, alkylthio, —N₃; —NO₂, amino, alkylamino, or dialkylamino; each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and n is an integer in the range of 0 to 8, inclusive; provided that when R₉ is —OR_(C), R₁₀, and R₁₁ are not simultaneously hydrogen. 95-96. (canceled)
 97. A pharmaceutical composition comprising a compound of claim 1 and a pharmaceutically acceptable excipient.
 98. A method of treating an infection, the method comprising steps of: administering an amount of the compound of claim 1 sufficient to cure the infection. 99-104. (canceled)
 105. A method of preparing an enone of formula (VII):

wherein R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or R₃ and R₄ are taken together to form ═O; R₅, R₉, R₁₀, and R₁₁ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and each R_(P) is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; the method comprising steps of: (a) deprotonating an isoxazole of formula (I):

with a suitable base under suitable conditions and reacting it with an enone of formula (II):

wherein each occurrence of R_(Q) is independently hydrogen, a C₁₋₆ alkyl, —Si(OR_(Z))₃, or —Si(R_(Z))₃, wherein each occurrence of R_(Z) is independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; or a substituted or unsubstituted, branched or unbranched heteroaryl; to yield a compound of formula (III):

wherein M is a counterion generated by the suitable base; (b) treating the compound of formula (III) with a suitable base under suitable conditions to yield a compound of formula (IV):

(c) heating the compound (IV) in a suitable solvent to yield a compound of formula (V):

(d) deprotonating the compound of formula (V) with a suitable base under suitable conditions and reacting with an electrophile to give a enone of formula (VI):

wherein R₁₀ is hydrogen; (e) optionally treating the enone of formula (VI) with a suitable reagent to give a 1,4-addition product of formula (VI) wherein R₁₀ is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; (f) treating the enone (VI) with a suitable acid under suitable conditions to epimerize R₅ and yield the enone of formula (VII). 106-109. (canceled)
 110. A method of preparing an enone of formula (VIIa):

wherein R₅ and R₁₀ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₉ is alkyl; R₁₁ is hydrogen; and R_(P) is hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; the method comprising steps of: (a) providing a compound of formula:

wherein each occurrence of R_(Q) is independently hydrogen, a C₁₋₆ alkyl, —Si(OR_(Z))₃, or —Si(R_(Z))₃, wherein each occurrence of R_(Z) is independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; or a substituted or unsubstituted, branched or unbranched heteroaryl; (b) performing an allylic displacement with an organocuprate reagent to give a compound of formula:

(c) oxidizing the alcohol moiety with an oxidant to give a compound of formula:

(d) treating the resulting compound with a base to form an enone of formula (IIa):

wherein R₉ is alkyl; (e) deprotonating an isoxazole of formula (I):

with a suitable base under suitable conditions and reacting it with the enone of formula (IIa) from step (d) to yield a compound of formula (IVa):

(f) heating the compound (IVa) in a suitable solvent to yield a compound of formula (VI):

wherein R₁₀ is hydrogen; (g) optionally treating the enone of formula (VIa) with a suitable reagent to give a 1,4-addition product of formula (VIa) wherein R₁₀ is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; (h) treating the enone (VIa) with a suitable acid under suitable conditions to epimerize R₅ and yield the enone of formula (VIIa). 111-189. (canceled)
 190. A compound of formula (VII) or (VI):

wherein R₃ and R₄ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(B); —CH₂OR_(B); —CH₂R_(B); —CH₂N(R_(B))₂; ═C(R_(B))₂; ═O; —C(═O)R_(B); —CO₂R_(B); —CN; —SCN; —SR_(B); —SOR_(B); —SO₂R_(B); —N₃; —NO₂; —N(R_(B))₂; —NHC(O)R_(B); —NHSO₂R_(B); or —C(R_(B))₃; wherein each occurrence of R_(B) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; R₅, R₉, R₁₀, and R₁₁ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted, branched or unbranched acyl; substituted or unsubstituted, branched or unbranched aryl; substituted or unsubstituted, branched or unbranched heteroaryl; —OR_(C); —CH₂OR_(C); —CH₂R_(C); —CH₂N(R_(C))₂; ═C(R_(C))₂; —C(═O)R_(C); —CO₂R_(C); —CN; —SCN; —SR_(C); —SOR_(C); —SO₂R_(C); —N₃; —NO₂; —N(R_(C))₂; —NHC(O)R_(C); —NHSO₂R_(C); or —C(R_(C))₃; wherein each occurrence of R_(C) is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, haloaliphatic, acyl, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and R_(P) is hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, haloaliphatic, a protecting group, substituted or unsubstituted acyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; provided that when R₉ is —OR_(C), R₁₀, and R₁₁ are not simultaneously hydrogen. 191-256. (canceled) 